Agilent 5973 MS User Manual

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Agilent Technologies

Agilent 5975

Series MSD

Operation Manual



2 5975 Series MSD Operation Manual

Notices© Agilent Technologies, Inc. 2012

No part of this manual may be reproduced in

any form or by any means (including elec-

tronic storage and retrieval or translation

into a foreign language) without prior agree-

ment and written consent from Agilent

Technologies, Inc. as governed by United

States and international copyright laws.

Manual Part Number

G3170-90036

Edition

Fourth edition, June 2012

Replaces G3170-90030

Printed in USA

Agilent Technologies, Inc.

5301 Stevens Creek Boulevard

Santa Clara, CA 95052

Warranty

The material contained in this docu-ment is provided “as is,” and is sub-ject to being changed, without notice,in future editions. Further, to the max-imum extent permitted by applicablelaw, Agilent disclaims all warranties,

either express or implied, with regardto this manual and any informationcontained herein, including but notlimited to the implied warranties ofmerchantability and fitness for a par-ticular purpose. Agilent shall not beliable for errors or for incidental orconsequential damages in connec-tion with the furnishing, use, or per-formance of this document or of anyinformation contained herein. ShouldAgilent and the user have a separatewritten agreement with warrantyterms covering the material in thisdocument that conflict with theseterms, the warranty terms in the sep-arate agreement shall control.

Safety Notices

CAUTION

A CAUTION notice denotes a

hazard. It calls attention to an

operating procedure, practice, orthe like that, if not correctly

performed or adhered to, could

result in damage to the product or

loss of important data. Do not

proceed beyond a CAUTION notice

until the indicated conditions are

fully understood and met.

WARNING

A WARNING notice denotes a

hazard. It calls attention to an

operating procedure, practice, or

the like that, if not correctly

performed or adhered to, could

result in personal injury or death.

Do not proceed beyond a

WARNING notice until the

indicated conditions are fully

understood and met.



5975 Series MSD Operation Manual 3

About This ManualThis manual contains information for operating and

maintaining the Agilent 5975 Series Gas Chromatograph/Mass

Selective Detector (GC/MSD) system.

1 “Introduction”

Chapter 1 describes general information about the 5975 Series

MSDs, including a hardware description, general safety

warnings, and hydrogen safety information.

2 “Installing GC Columns”

Chapter 2 shows you how to prepare a capillary column for use

with the MSD, install it in the GC oven, and connect it to the

MSD using the GC/MSD interface.

3 “Operating in Electron Impact (EI) Mode”

Chapter 3 describes basic tasks such as setting temperatures,

monitoring pressures, tuning, venting, and pumpdown. Much of

the information in this chapter also applies to CI operation.

4 “Operating in Chemical Ionization (CI) Mode”

Chapter 4 describes additional tasks necessary to operate in CI

mode.

5 “General Maintenance”

Chapter 5 describes maintenance procedures common to both

EI and CI instruments.

6 “CI Maintenance”

Chapter 6 describes maintenance procedures unique to CI

MSDs.

A “Chemical Ionization Theory”

Appendix A is an overview of chemical ionization theory.




Online User InformationNow your Agilent instrument documentation is in one place, at

your fingertips.

The Instrument Utilities DVD that ships with your instrument

provides an extensive collection of online help, videos, and

books for the Agilent 7890A GC, 7820A GC, 6890N GC, 6850 GC, 5975T

LTM GC/MS, 7693A ALS, and the 7683B ALS. Included are localized

versions of the information you need most, such as:

• Getting Familiar documentation• Safety and Regulatory guides• Site Preparation checklists• Installation information• Operating guides• Maintenance information• Troubleshooting details




Contents

1 Introduction

5975 MSD Version 10

Abbreviations Used 11

The 5975 Series MSD 13

CI MSD Hardware Description 15

Important Safety Warnings 17

Hydrogen Safety 19

GC precautions 19

Safety and Regulatory Certifications 24

Cleaning/Recycling the Product 27

Liquid Spillage 27

Moving or Storing the MSD 27

2 Installing GC Columns

Columns 30

To reconfigure a 6850 GC column on its basket 32

To prepare a capillary column for installation 37

To install a capillary column in a split/splitless inlet 39

To condition a capillary column 41

To install a capillary column in the GC/MSD interface 43

Agilent 7890A and 7820A, and 6890 GCs 43

6850 GC 45

3 Operating in Electron Impact (EI) Mode

Operating the MSD from the Data System 51




Operating the MSD from the LCP 51Modes of operation 51

LCP Status Messages 53

ChemStation Loading <timestamp> 53

Executing <type>tune 53

Instrument Available <timestamp> 53

Loading Method <method name> 53Loading MSD Firmware 53

Loading OS 54

<method> Complete <timestamp> 54

Method Loaded <method name> 54

MS locked by <computer name> 54

Press Sideplate 54

Run: <method> Acquiring <datafile> 54

To view system status during startup 54

LCP Menus 55

The EI GC/MSD Interface 58

Before You Turn On the MSD 60

Pumping Down 61

Controlling Temperatures 61

Controlling Column Flow 62

Venting the MSD 63

To view MSD analyzer temperature and vacuum status 64

To set monitors for MSD temperature and vacuum status 66

To set the MSD analyzer temperatures 67

To set the GC/MSD interface temperature from the

ChemStation 69

To monitor high vacuum pressure 71




To measure column flow linear velocity 73

To confirm column flow 74

To tune the MSD 75

To verify system performance 76

High-Mass Testing (5975 Series MSDs) 77

To remove the MSD covers 80

To vent the MSD 82

To open the analyzer chamber 84

To close the analyzer chamber 87

To pump down the MSD 91

To move or store the MSD 93

To set the interface temperature from the GC 95

4 Operating in Chemical Ionization (CI) Mode

General Guidelines 98

The CI GC/MSD Interface 99To Operate the CI MSD 101

To switch from the EI source to the CI source 102

To pump down the CI MSD 103

To set up the software for CI operation 104

To operate the reagent gas flow control module 106

To set up methane reagent gas flow 109

To use other reagent gases 111

To switch from the CI source to the EI source 115

CI Autotune 116




To perform a PCI autotune (methane only) 118

To perform an NCI autotune (methane reagent gas) 120

To verify PCI performance 122

To verify NCI performance 123


5 General Maintenance

Before Starting 128

Maintaining the Vacuum System 133

6 CI Maintenance

General Information 140To Set Up Your MSD for CI Operation 141

A Chemical Ionization Theory

Chemical Ionization Overview 146

Positive CI Theory 148

Negative CI Theory 155



9

Agilent 5975 Series MSD

Operation Manual


1

Introduction

5975 MSD Version 10

Abbreviations Used 11

The 5975 Series MSD 13CI MSD Hardware Description 15

Important Safety Warnings 17

Many internal parts of the MSD carry dangerous voltages 17

Electrostatic discharge is a threat to MSD electronics 17

Many parts are dangerously hot 18

The oil pan under the standard foreline pump can be a fire hazard 18

Hydrogen Safety 19

Dangers unique to GC/MSD operation 20

Hydrogen accumulation in an MSD 20

Precautions 22

Safety and Regulatory Certifications 24

Information 24

Symbols 25

Electromagnetic compatibility 26

Sound emission declaration 26

Cleaning/Recycling the Product 27

Liquid Spillage 27

Moving or Storing the MSD 27

This manual describes the operation, and routine maintenance of the Agilent

Technologies 5975 Series MSD.




1 Introduction

5975 MSD Version

5975 Series MSDs are equipped with a diffusion pump or one of two

turbomolecular (turbo) pumps. The serial number label displays a product

number (Table 1) that indicates what kind of MSD you have.

Table 1 Available high vacuum pumps

Model name Product number Description Ionization modes

5975C TAD VL MSD G3170A Diffusion Pump MSD Electron impact (EI)

5975C TAD inert

MSD

5975C TAD inert XL

MSD

G3171A

G3172A

Standard Turbo MSD

Performance Turbo MSD

Electron impact (EI)


5975C TAD inert XL

MSD

G3174A CI High Mass Performance

Turbo Pump


Negative chemical ionization (NCI)

Positive chemical ionization (PCI)

7820 MSD VL G3175A Diffusion Pump MSD Electron impact (EI)

7820 MSD G3176A Standard Turbo MSD Electron impact (EI)



Introduction 1


Abbreviations Used

The abbreviations in Table 2 are used in discussing this product. They are

collected here for convenience.

Table 2 Abbreviations

Abbreviation Definition

AC Alternating current

ALS Automatic liquid sampler

BFB Bromofluorobenzene (calibrant)

CI Chemical ionization

DC Direct current

DFTPP Decafluorotriphenylphosphine (calibrant)

DIP Direct insertion probe

DP Diffusion pump

EI Electron impact ionization

EM Electron multiplier (detector)

EMV Electron multiplier voltage

EPC Electronic pneumatic control

eV Electron volt

GC Gas chromatograph

HED High-energy dynode (refers to detector and its power supply)

id Inside diameter

LAN Local Area Network

LCP Local control panel (on the MSD)

LTM Low thermal mass

m/z Mass to charge ratio

MFC Mass flow controller




1 Introduction

MSD Mass Selective Detector

NCI Negative CI

OFN Octafluoronaphthalene (calibrant)

PCI Positive CI

PFDTD Perfluoro-5,8-dimethyl-3,6,9-trioxydodecane (calibrant)

PFHT 2,4,6-tris(perfluoroheptyl)-1,3,5-triazine (calibrant)

PFTBA Perfluorotributylamine (calibrant)

Quad Quadrupole mass filter

RF Radio frequency

RFPA Radio frequency power amplifier

Torr Unit of pressure, 1 mm Hg

Turbo Turbomolecular (pump)

Table 2 Abbreviations (continued)

Abbreviation Definition



Introduction 1


The 5975 Series MSD

The 5975 Series MSD is a stand-alone capillary GC detector for use with an

Agilent Series Gas Chromatograph (Table 3). The MSD features:

• Local Control Panel (LCP) for locally monitoring and operating the MSD

• One of three different high vacuum pumps

• Rotary vane foreline pump

• Independently MSD heated electron-ionization ion source

• Independently MSD heated hyperbolic quadrupole mass filter

• High-energy dynode (HED) electron multiplier detector

• Independently GC heated GC/MSD interface

• Chemical ionization (EI/PCI/NCI) modes available

Physical description

The 5975 Series MSD is a rectangular box, approximately 42 cm high, 26 cm

wide, and 65 cm deep. The weight is 25 kg for the diffusion pump mainframe,

26 kg for the standard turbo pump mainframe, and 29 kg for the performance

turbo pump mainframe. The attached foreline (roughing) pump weighs an

additional 11 kg (standard pump).

The basic components of the instrument are: the frame/cover assemblies, thelocal control panel, the vacuum system, the GC interface, the electronics, and

the analyzer.

Local control panel

The local control panel allows local monitoring and operation of the MSD. You

can tune the MSD, run a method or a sequence, and monitor instrument

status.

Vacuum gauge

The 5975 Series MSD may be equipped with a Micro-Ion Vacuum Gauge. The

MSD ChemStation can be used to read the pressure (high vacuum) in the

vacuum manifold. Operation of the gauge controller is described in this

manual.




1 Introduction

The gauge is required for chemical ionization (CI) operation.

Table 3 5975 series MSD models and features

Model

Feature G3170A

G3175A

G3171A

G3176A

G3172A G3174A

High vacuum pump Diffusion Standard

turbo

Performance

turbo

Performance

turbo

Optimal He column flow mL/min 1 1 1 to 2 1 to 2

Maximum recommended gas flow

mL/min*

* Total gas flow into the MSD: column flow plus reagent gas flow (if applicable).

1.5 2.0 4.0 4

Maximum gas flow, mL/min†

† Expect degradation of spectral performance and sensitivity.

2 2.4 6.5 6.5

Max column id 0.25 mm

(30 m)

0.32 mm

(30 m)

0.53 mm

(30 m)

0.53 mm

(30 m)

CI capability No No No Yes

DIP‡ capability (3rd party)

‡ Direct insertion probe.

Yes Yes Yes Yes



Introduction 1


CI MSD Hardware Description

Figure 1 is an overview of a typical 5975 GC/MSD system.

The CI hardware allows the 5975 Series MSD to produce high-quality, classical

CI spectra, which include molecular adduct ions. A variety of reagent gases

can be used.

Figure 1 5975 Series GC/MSD system

ALS

7890A GC

CI gas flow module

Local control panel

5975 Series MSD

MSD power switch

GC power switch




1 Introduction

In this manual, the term “CI MSD” refers to the G3174A MSD and upgraded

G3172A MSDs. It also applies, unless otherwise specified, to the flow modulesfor these instruments.

The 5975 Series CI system adds to the 5975 Series MSD:

• EI/CI GC/MSD interface

• CI ion source and interface tip seal

• Reagent gas flow control module

• Bipolar HED power supply for PCI and NCI operation

A methane/isobutane gas purifier is provided and is required . It removes

oxygen, water, hydrocarbons, and sulfur compounds.

A high vacuum gauge controller (G3397A) is required for CI MSD and is

recommended for EI also.

The MSD CI system has been optimized to achieve the relatively high source

pressure required for CI while still maintaining high vacuum in thequadrupole and detector. Special seals along the f low path of the reagent gas

and very small openings in the ion source keep the source gases in the

ionization volume long enough for the appropriate reactions to occur.

The CI interface has special plumbing for reagent gas. A spring-loaded

insulating seal fits onto the tip of the interface.

Switching back and forth between CI and EI sources takes less than an hour,

although a 1- to 2-hour wait is required to purge the reagent gas lines and bake

out water and other contaminants. Switching from PCI to NCI requires about

2 hours for the ion source to cool.



Introduction 1


Important Safety WarningsThere are several important safety notices to always keep in mind when using

the MSD.

Many internal parts of the MSD carry dangerous voltages

If the MSD is connected to a power source, even if the power switch is off,

potentially dangerous voltages exist on:

• The wiring between the MSD power cord and the AC power supply, the AC

power supply itself, and the wiring from the AC power supply to the power

switch.

With the power switch on, potentially dangerous voltages also exist on:

• All electronics boards in the instrument.

• The internal wires and cables connected to these boards.• The wires for any heater (oven, detector, inlet, or valve box).

Electrostatic discharge is a threat to MSD electronics

The printed circuit boards in the MSD can be damaged by electrostaticdischarge. Do not touch any of the boards unless it is absolutely necessary. If

you must handle them, wear a grounded wrist strap and take other antistatic

precautions. Wear a grounded wrist strap any time you must remove the MSD

right side cover.

WARNINGAll these parts are shielded by covers. With the covers in place, it should be difficult

to accidentally make contact with dangerous voltages. Unless specifically

instructed to, never remove a cover unless the detector, inlet, or oven are turned off.

WARNINGIf the power cord insulation is frayed or worn, the cord must be replaced. Contact

your Agilent service representative.




1 Introduction

Many parts are dangerously hot

Many parts of the GC/MSD operate at temperatures high enough to cause

serious burns. These parts include but are not limited to:

• The inlets

• The oven and its contents

• The detector

• The column nuts attaching the column to an inlet or detector

• The valve box

• The foreline pump

Always cool these areas of the system to room temperature before working on

them. They will cool faster if you first set the temperature of the heated zone

to room temperature. Turn the zone off after it has reached the setpoint. If you

must perform maintenance on hot parts, use a wrench and wear gloves.

Whenever possible, cool the part of the instrument that you will bemaintaining before you begin working on it.

The oil pan under the standard foreline pump can be a fire hazard

Oily rags, paper towels, and similar absorbents in the oil pan could ignite and

damage the pump and other parts of the MSD.

WARNINGBe careful when working behind the instrument. During cool-down cycles, the GC

emits hot exhaust which can cause burns.

WARNING The insulation around the inlets, detectors, valve box, and the insulation cups ismade of refractory ceramic fibers. To avoid inhaling fiber particles, we recommend

the following safety procedures: ventilate your work area; wear long sleeves,

gloves, safety glasses, and a disposable dust/mist respirator; dispose of insulation

in a sealed plastic bag; wash your hands with mild soap and cold water after

handling the insulation.

WARNINGCombustible materials (or flammable/non-flammable wicking material) placed

under, over, or around the foreline (roughing) pump constitutes a fire hazard. Keep

the pan clean, but do not leave absorbent material such as paper towels in it.



Introduction 1


Hydrogen Safety

Hydrogen is a commonly used GC carrier gas. Hydrogen is potentially

explosive and has other dangerous characteristics.

• Hydrogen is combustible over a wide range of concentrations. At

atmospheric pressure, hydrogen is combustible at concentrations from 4%

to 74.2% by volume.

• Hydrogen has the highest burning velocity of any gas.

• Hydrogen has a very low ignition energy.

• Hydrogen that is allowed to expand rapidly from high pressure can

self-ignite.

• Hydrogen burns with a nonluminous flame which can be invisible under

bright light.

GC precautions

When using hydrogen as a carrier gas, remove the large round plastic cover for

the MSD transfer line located on the GC left side panel. In the unlikely event of

an explosion, this cover may dislodge.

WARNINGThe use of hydrogen as a GC carrier gas is potentially dangerous.

WARNING When using hydrogen (H2) as the carrier gas or fuel gas, be aware that hydrogengas can flow into the GC oven and create an explosion hazard. Therefore, be sure

that the supply is turned off until all connections are made and ensure that the inlet

and detector column fittings are either connected to a column or capped at all times

when hydrogen gas is supplied to the instrument.

Hydrogen is flammable. Leaks, when confined in an enclosed space, may create a

fire or explosion hazard. In any application using hydrogen, leak test all

connections, lines, and valves before operating the instrument. Always turn off thehydrogen supply at its source before working on the instrument.




1 Introduction

Dangers unique to GC/MSD operation

Hydrogen presents a number of dangers. Some are general, others are unique

to GC or GC/MSD operation. Dangers include, but are not limited to:

• Combustion of leaking hydrogen.

• Combustion due to rapid expansion of hydrogen from a high-pressure

cylinder.

• Accumulation of hydrogen in the GC oven and subsequent combustion (see

your GC documentation and the label on the top edge of the GC oven door).

• Accumulation of hydrogen in the MSD and subsequent combustion.

Hydrogen accumulation in an MSD

All users should be aware of the mechanisms by which hydrogen can

accumulate (Table 4) and know what precautions to take if they know or

suspect that hydrogen has accumulated. Note that these mechanisms apply to

all mass spectrometers, including the MSD.

WARNINGThe MSD cannot detect leaks in inlet and/or detector gas streams. For this reason,

it is vital that column fittings should always be either connected to a column or havea cap or plug installed.

Table 4 Hydrogen accumulation mechanisms

Mechanism Results

Mass spectrometer turned off A mass spectrometer can be shut down

deliberately. It can also be shut down accidentally

by an internal or external failure. A massspectrometer shutdown does not shut off the flow

of carrier gas. As a result, hydrogen may slowly

accumulate in the mass spectrometer.



Introduction 1


Mass spectrometer automated shutoff

valves closed

Some mass spectrometers are equipped with

automated diffusion pump shutoff valves. In these

instruments, deliberate operator action or various

failures can cause the shutoff valves to close.

Shutoff valve closure does not shut off the flow of

carrier gas. As a result, hydrogen may slowlyaccumulate in the mass spectrometer.

Mass spectrometer manual shutoff

valves closed

Some mass spectrometers are equipped with

manual diffusion pump shutoff valves. In these

instruments, the operator can close the shutoff

valves. Closing the shutoff valves does not shut off

the flow of carrier gas. As a result, hydrogen mayslowly accumulate in the mass spectrometer.

GC off A GC can be shut down deliberately. It can also be

shut down accidentally by an internal or external

failure. Different GCs react in different ways. If a

6890 GC equipped with Electronic Pressure Control

(EPC) is shut off, the EPC stops the flow of carriergas. If the carrier flow is not under EPC control, the

flow increases to its maximum. This flow may be

more than some mass spectrometers can pump

away, resulting in the accumulation of hydrogen in

the mass spectrometer. If the mass spectrometer is

shut off at the same time, the accumulation can be

fairly rapid.

Power failure If the power fails, both the GC and mass

spectrometer shut down. The carrier gas, however,

is not necessarily shut down. As described

previously, in some GCs a power failure may cause

the carrier gas flow to be set to maximum. As a

result, hydrogen may accumulate in the mass

spectrometer.

Table 4 Hydrogen accumulation mechanisms (continued)

Mechanism Results




1 Introduction

Precautions

Take the following precautions when operating a GC/MSD system with

hydrogen carrier gas.

Equipment precaution

You MUST make sure the front side-plate thumbscrew is fastened finger-tight.

Do not overtighten the thumbscrew; it can cause air leaks.

You must remove the plastic cover over the glass window on the front of a 5975

MSD. In the unlikely event of an explosion, this cover may dislodge.

General laboratory precautions

• Avoid leaks in the carrier gas lines. Use leak-checking equipment toperiodically check for hydrogen leaks.

• Eliminate from your laboratory as many ignition sources as possible (open

flames, devices that can spark, sources of static electricity, etc.).

• Do not allow hydrogen from a high pressure cylinder to vent directly to

atmosphere (danger of self-ignition).

• Use a hydrogen generator instead of bottled hydrogen.

WARNING Once hydrogen has accumulated in a mass spectrometer, extreme caution must beused when removing it. Incorrect startup of a mass spectrometer filled with

hydrogen can cause an explosion.

WARNINGAfter a power failure, the mass spectrometer may start up and begin the pumpdown

process by itself. This does not guarantee that all hydrogen has been removed from

the system or that the explosion hazard has been removed.

WARNINGFailure to secure your MSD as described above greatly increases the chance of

personal injury in the event of an explosion.



Introduction 1


Operating precautions

• Turn off the hydrogen at its source every time you shut down the GC or

MSD.

• Turn off the hydrogen at its source every time you vent the MSD (do not

heat the capillary column without carrier gas f low).

• Turn off the hydrogen at its source every time shutoff valves in an MSD are

closed (do not heat the capillary column without carrier gas flow).

• Turn off the hydrogen at its source if a power failure occurs.• If a power failure occurs while the GC/MSD system is unattended, even if

the system has restarted by itself:

1 Immediately turn off the hydrogen at its source.

2 Turn off the GC.

3 Turn off the MSD and allow it to cool for 1 hour.

4 Eliminate all potential sources of ignition in the room.5 Open the vacuum manifold of the MSD to atmosphere.

6 Wait at least 10 minutes to allow any hydrogen to dissipate.

7 Start up the GC and MSD as normal.

When using hydrogen gascheck the system for leaks to prevent possible fire

and explosion hazards based on local Environmental Health and Safety (EHS)

requirements. Always check for leaks after changing a tank or servicing the

gas lines. Always make sure the vent line is vented into a fume hood.




1 Introduction

Safety and Regulatory Certifications

The 5975 Series MSD conforms to the following safety standards:

• Canadian Standards Association (CSA): CAN/CSA-C222 No. 61010-1-04

• CSA/Nationally Recognized Test Laboratory (NRTL): UL 61010–1

• International Electrotechnical Commission (IEC): 61010–1

• EuroNorm (EN): 61010–1

The 5975 MSD conforms to the following regulations on Electromagnetic

Compatibility (EMC) and Radio Frequency Interference (RFI):

• CISPR 11/EN 55011: Group 1, Class A

• IEC/EN 61326

• AUS/NZ

This ISM device complies with Canadian ICES-001. Cet appareil ISM est conforme a la norme NMB—001 du Canada.

The 5975 Series MSD is designed and manufactured under a quality system

registered to ISO 9001.

Information

The Agilent Technologies 5975 Series MSD meets the following IEC

(International Electro-technical Commission) classifications: Equipment Class

I, Laboratory Equipment, Installation Category II, Pollution Degree 2.

This unit has been designed and tested in accordance with recognized safety

standards and is designed for use indoors. If the instrument is used in a

manner not specified by the manufacturer, the protection provided by theinstrument may be impaired. Whenever the safety protection of the MSD has

been compromised, disconnect the unit from all power sources and secure the

unit against unintended operation.

Refer servicing to qualified service personnel. Substituting parts or

performing any unauthorized modification to the instrument may result in a

safety hazard.



Introduction 1


Symbols

Warnings in the manual or on the instrument must be observed during all

phases of operation, service, and repair of this instrument. Failure to comply

with these precautions violates safety standards of design and the intended

use of the instrument. Agilent Technologies assumes no liability for the

customer’s failure to comply with these requirements.

See accompanying instructions for more information.

Indicates a hot surface.

Indicates hazardous voltages.

Indicates earth (ground) terminal.

Indicates potential explosion hazard.

Indicates radioactivity hazard.

Indicates electrostatic discharge hazard.

Indicates that you must not discard this

electrical/electronic product in domestic household

waste.

or




1 Introduction

Electromagnetic compatibility

This device complies with the requirements of CISPR 11. Operation is subject

to the following two conditions:

• This device may not cause harmful interference.

• This device must accept any interference received, including interference

that may cause undesired operation.

If this equipment does cause harmful interference to radio or television

reception, which can be determined by turning the equipment off and on, theuser is encouraged to try one or more of the following measures:

1 Relocate the radio or antenna.

2 Move the device away from the radio or television.

3 Plug the device into a different electrical outlet, so that the device and the

radio or television are on separate electrical circuits.

4 Make sure that all peripheral devices are also certified.5 Make sure that appropriate cables are used to connect the device to

peripheral equipment.

6 Consult your equipment dealer, Agilent Technologies, or an experienced

technician for assistance.

7 Changes or modifications not expressly approved by Agilent Technologies

could void the user’s authority to operate the equipment.

Sound emission declaration

Sound pressure

Sound pressure Lp <70 dB according to EN 27779:1991.

Schalldruckpegel

Schalldruckpegel LP <70 dB am nach EN 27779:1991.



Introduction 1


Cleaning/Recycling the Product

To clean the unit, disconnect the power and wipe down with a damp, lint-free

cloth. For recycling, contact your local Agilent sales office.

Liquid Spillage

Do not spill liquids on the MSD.

Moving or Storing the MSD

The best way to keep your MSD functioning properly is to keep it pumped

down and hot, with carrier gas flow. If you plan to move or store your MSD, a

few additional precautions are required. The MSD must remain upright at all

times; this requires special caution when moving. The MSD should not be left

vented to atmosphere for long periods.

1




1 Introduction

A il t 5975 S i MSD



29


Operation Manual


2

Installing GC Columns

Columns 30

Conditioning columns 30

Conditioning ferrules 31Tips and hints 31

To reconfigure a 6850 GC column on its basket 32

To prepare a capillary column for installation 37

To install a capillary column in a split/splitless inlet 39

To condition a capillary column 41

To install a capillary column in the GC/MSD interface 43

Before you can operate your GC/MSD system, you must select, install, and

condition a GC column. This chapter will show you how to install and

condition a column. For correct column and flow selection, you must know

what type of vacuum system your MSD has. The serial number tag on the lower

front of the left side panel shows the model number.






Columns

Many types of GC columns can be used with the MSD but there are some

restrictions.

During tuning or data acquisition the rate of column flow into the MSD should

not exceed the maximum recommended flow. Therefore, there are limits to

column length and flow. Exceeding recommended flow will result in

degradation of mass spectral and sensitivity performance.

Remember that column flows vary greatly with oven temperature. See “To

measure column flow linear velocity” for instructions on how to measure

actual flow in your column. Use the Flow Calculation software and Table 5 to

determine whether a given column will give acceptable flow with realistic

head pressure.

Conditioning columns

Conditioning a column before it is connected to the GC/MSD interface is

essential.

Table 5 Gas flows

Feature G3170A

G3175A

G3171A

G3176A

G3172A G3174A

High vacuum pump Diffusion Standard

turbo

Performance

turbo

Performance

turbo

Optimal gas flow, mL/min*

* Total gas flow into the MSD = column flow + reagent gas flow (if applicable)

1 1 1 to 2 1 to 2

Maximum recommended gas flow,mL/min

1.5 2 4 4

Maximum gas flow, mL/min†

† Expect degradation of spectral performance and sensitivity.

2 2.4 6.5 6.5

Maximum column id 0.25 mm

(30 m)

0.32 mm

(30 m)

0.53 mm

(30 m)

0.53 mm

(30 m)

Installing GC Columns 2

http://localhost/var/www/apps/conversion/tmp/Videos/Condition%20capillary%20column.wmv







A small portion of the capillary column stationary phase is often carried away

by the carrier gas. This is called column bleed. Column bleed deposits traces of the stationary phase in the MSD ion source. This decreases MSD sensitivity

and makes cleaning the ion source necessary.

Column bleed is most common in new or poorly crosslinked columns. It is

much worse if there are traces of oxygen in the carrier gas when the column is

heated. To minimize column bleed, all capillary columns should be

conditioned before they are installed in the GC/MSD interface.

Conditioning ferrules

Heating ferrules to their maximum expected operating temperature a few

times before they are installed can reduce chemical bleed from the ferrules.

Tips and hints

• The column installation procedures for the 5975 Series MSDs is different from that for previous MSDs. Using the procedure from another instrument

may not work and may damage the column or the MSD.

• You can remove old ferrules from column nuts with an ordinary push pin.

• Always use carrier gas that is at least 99.9995% pure.

• Because of thermal expansion, new ferrules may loosen after heating and

cooling a few times. Check for tightness after two or three heating cycles.

• Always wear clean gloves when handling columns, especially the end that

will be inserted into the GC/MSD interface.

WARNINGIf you are using hydrogen as a carrier gas, do not start carrier gas flow until the

column is installed in the MSD and the MSD has been pumped down. If the vacuum

pumps are off, hydrogen will accumulate in the MSD and an explosion may occur.

See “Hydrogen Safety” .

WARNINGAlways wear safety glasses when handling capillary columns. Use care to avoid

puncturing your skin with the end of the column.






To reconfigure a 6850 GC column on its basket

Before installing a 6850, first reconfigure it to better position the column ends

for installation in the GC MSD interface.

1 Lay the column (19091S-433E found in the GC ship kit) on a clean surface

with the column label facing the user in the 12 o’clock position. Note that

the inlet and outlet ends of the column are oriented the same as when a GC

detector is used and the column outlet is positioned at the back (closer to

the fan) of the column cage holder. See Figure 2.

Figure 2 Column

Column inlet

Column outlet

6850 column nut




g


2 Remove the septum cap from the column OUTLET side and uncoil 2 column

loops. See Figure 3.

3 Attach three column clips (part number G2630-20890) to the column cage

as follows:• Attach one clip onto the back of the 1 o’clock cross-member piece of the

column cage.

• Attach two clips onto the front of the 3 o’clock cross-member piece of the

column cage.

These clips will help provide appropriate orientation of column ends for

their insertion into the GC inlet and MSD interface.

Figure 3 Column with 2 uncoiled loops

1 o’clock cross-member

3 o’clock cross-member





See Figure 4.

4 Feed the outlet side of the column through the 1 o’clock positioned clip sothat the column outlet is pointing toward the front of the column cage. See

Figure 5.

Figure 4 Column with column clips attached

Column clip

(1 o’clock postion)

Column clips

(3 o’clock position)

Column outlet

CAUTIONBe careful not to scratch the column coating.





5 Next, feed the outlet side of the column through the 3 o’clock positioned

clips so that the column outlet is pointing toward the back of the column

cage. Make sure that the part of the column that is between the two clips

does NOT extend above the column label. See Figure 6.

Figure 5 Column fed through 1 o’clock position

To column outlet

Column clip


Column clips


CAUTIONBe careful not to scratch the column coating.





There should be approximately 50 cm of column extending beyond the

3 o’clock positioned clip.

6 Carefully rewind the remainder of the column outlet end around thecolumn cage.

Figure 6 Column fed through 3 o’clock position

Column clip

(1 o’clock postion)

Column clips


To column outlet

(at least 50 cm)





To prepare a capillary column for installation

Materials needed

• Capillary column

• Column cutter, ceramic (5181-8836) or diamond (5183-4620)

• Ferrules

• 0.27-mm id, for 0.10-mm id columns (5062-3518)





• Gloves, clean

• Large (8650-0030)

• Small (8650-0029)

• Inlet column nut (5181-8830 for Agilent 7890A, 7820A and 6890, or

5183-4732 for 6850)

• Magnifying loupe

• Septum (may be old, used inlet septum)

Procedure

1 Slide a septum, column nut, and conditioned ferrule onto the free end of the

column (Figure 7). The tapered end of the ferrule should point away from

the column nut.





2 Use the column cutter to score the column 2 cm from the end.

3 Break off the end of the column. Hold the column against the column cutter

with your thumb. Break the column against the edge of the column cutter.

4 Inspect the end for jagged edges or burrs. If the break is not clean and even,

repeat steps 2 and 3.5 Wipe the outside of the free end of the column with a lint-free cloth

moistened with methanol.

Figure 7 Preparing a capillary column for installation

Capillary column

Column cutter

Ferrule, taper up

Inlet column nut

Septum





To install a capillary column in a split/splitless inlet

Materials needed

• Gloves, clean

• Large (8650-0030)

• Small (8650-0029)

• Metric ruler

• Wrench, open-end, 1/4-inch and 5/16-inch (8710-0510)

To install columns in other types of inlets, refer to your Gas Chromatograph

User Information.

Procedure

1 Prepare the column for installation ( “To prepare a capillary column for

installation” on page 37).

2 Position the column so it extends 4 to 6 mm past the end of the ferrule

(Figure 8).

Figure 8 Installing a capillary column for a split/splitless inlet

Insulation cup

Reducing nut

Capillary column

Ferrule (inside nut)

Inlet column nut

Septum

4 to 6 mm


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3 Slide the septum to place the nut and ferrule in the correct position.

4 Insert the column in the inlet.

5 Slide the nut up the column to the inlet base and finger-tighten the nut.

6 Adjust the column position so the septum is even with the bottom of the

column nut.

7 Tighten the column nut an additional 1/4 to 1/2 turn. The column should

not slide with a gentle tug.

8 Start carrier gas flow.9 Verify flow by submerging the free end of the column in isopropanol. Look

for bubbles.





To condition a capillary column

Materials needed

• Carrier gas, (99.9995% pure or better)


Procedure

1 Install the column in the GC inlet ( “To install a capillary column in asplit/splitless inlet” on page 39).

2 Allow the carrier gas to flow through the column for 5 minutes without

heating the GC oven.

3 Ramp the oven temperature at 5 °C/minute to 10 °C above your highest

analytical temperature.

4 Once the oven temperature exceeds 80 °C, inject 5 µL methanol into the GC.

Repeat two more times at 5-minute intervals. This helps remove any contamination from the column before it is installed into the GC/MSD

interface.

5 Hold this temperature. Allow the carrier gas to flow for several hours.

6 Return the GC oven temperature to a low standby temperature.

WARNING

Do not condition your capillary column with hydrogen. Hydrogen accumulation in

the GC oven can result in an explosion. If you plan to use hydrogen as your carrier

gas, first condition the column with ultrapure (99.999% or better) inert gas such as

helium, nitrogen, or argon.

CAUTIONNever exceed the maximum column temperature, either in the GC/MSD interface, the

GC oven, or the inlet.








See also

For more information about installing a capillary column, refer to the

application note Optimizing Splitless Injections on Your GC for High

Performance MS Analysis, publication number 5988-9944EN.





To install a capillary column in the GC/MSD interface

Agilent 7890A and 7820A, and 6890 GCs

Materials needed

• Column cutter, ceramic (5181-8836) or diamond (5183-4620)

• Ferrules


• 0.4-mm id, for 0.20- and 0.25-mm id columns (5062-3508)



• Flashlight

• Hand lens (magnifying loupe)

• Gloves, clean

• Large (8650-0030)

• Small (8650-0029)

• Interface column nut (05988-20066)

• Safety glasses


Procedure

1 Condition the column (page 41).

2 Vent the MSD (page 82) and open the analyzer chamber (page 84). Be sure

you can see the end of the GC/MSD interface.

3 If the CI interface is installed, remove the spring-loaded tip seal from the

MSD end of the interface.

4 Slide an interface nut and conditioned ferrule onto the free end of the GC

column. The tapered end of the ferrule must point towards the nut.

CAUTIONNote that the column installation procedure for the 5975 Series MSDs is different from

that for most previous MSDs. Using the procedure from another instrument may result

in poor sensitivity and possible damage to the MSD.


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5 Slide the column into the GC/MSD interface (Figure 9) until you can pull it

out through the analyzer chamber.

6 Break 1 cm off the end of the column (page 32). Do not let any column

fragments fall into the analyzer chamber. They could damage the high

vacuum pump.

7 Clean the outside of the free end of the column with a lint-free cloth

moistened with methanol.8 Adjust the column so it projects 1 to 2 mm past the end of the interface.

Use the flashlight and hand lens if necessary to see the end of the column

inside the analyzer chamber. Do not use your finger to feel for the column

end.

Figure 9 Installing a capillary column in the GC/MSD interface

1 to 2 mm

GC/MSD interface

(MSD end)

Analyzer chamber

GC/MSD interface

(GC end)

Interface column nut

Column

MSD GC Oven





9 Hand-tighten the nut. Make sure the position of the column does not change

as you tighten the nut. Reinstall the spring-loaded tip seal if it was removedearlier.

10 Check the GC oven to be sure that the column does not touch the oven

walls.

11 Tighten the nut 1/4 to 1/2 turn. Check the tightness after one or two heat

cycles.

6850 GC1 Carefully unwind the outlet end of the GC column until the

3 o’clock clip is reached.

2 Slide an interface column nut (part number 05988-20066) and ferrule (part

number 5062-3508) onto the outlet end of the GC column.

The tapered end of the ferrule must point towards the nut.

3 Slide the column into the GC/MSD interface until the column protrudesinto the analyzer chamber at least 5 cm.

4 Adjust the length of the column from the 3 o’clock clip to the back of the

interface column nut to be 22–28 cm. See Figure 10.

5 Hand tighten the interface nut.

6 Carefully close the oven door while observing to see that the column does

not develop sharp bends or touch the oven walls/floor. Try this procedure

several times.


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7 Loosen the interface nut and push the column an additional 3–5 cm into

the analyzer chamber.

8 Make a clean cut of the column so that now only 3–5 cm protrudes into theanalyzer chamber.

9 Clean the outside of the free end of the column with a lint-free cloth

moistened with methanol.

10 Adjust the column so that it protrudes 1 to 2 mm into the analyzer chamber

past the end of the GC/MSD interface, and hand tighten the nut. See

Figure 11.

Make sure the position of the column does not change as you retighten the

nut.

Figure 10 Oven door opened and closed

22–28 cm from 3 o’clock clip to GC/MSD interface nut





11 Repeat step 6 to assure column integrity.

12 Tighten the interface nut an additional 1/4 to 1/2 turn with a 1/4-inch

open-end wrench.

Check the tightness after one or two heat cycles.

13 Turn the GC on.

14 Verify that the inlet temperature is set to 25 °C.15 Close the analyzer side plate, then reconnect the source power and side

board control cables.

16 Turn on the MSD power switch to initiate MSD pump down.

Press on the side plate of the MSD to achieve a good seal. Verify that the

foreline pump and front fan turn on and that the foreline pump stops

gurgling within 60 seconds.

Figure 11 MSD - GC column connection

1 to 2 mm

GC/MSD interface

(MSD end)

Analyzer chamber

GC/MSD interface

(GC end)

Interface column nut

Column

MSD GC Oven





17 Reinstall the MSD analyzer cover.


Operation Manual



49Agilent Technologies

3Operating in Electron Impact (EI) Mode

Operating the MSD from the Data System 51

Operating the MSD from the LCP 51

LCP Status Messages 53

LCP Menus 55

The EI GC/MSD Interface 58

Before You Turn On the MSD 60

Pumping Down 61

Controlling Temperatures 61

Controlling Column Flow 62

Venting the MSD 63

To view MSD analyzer temperature and vacuum status 64

To set monitors for MSD temperature and vacuum status 66

To set the MSD analyzer temperatures 67

To set the GC/MSD interface temperature from the ChemStation 69


To measure column flow linear velocity 73

To confirm column flow 74To tune the MSD 75

To verify system performance 76

High-Mass Testing (5975 Series MSDs) 77

To remove the MSD covers 80

To vent the MSD 82

To open the analyzer chamber 84

To close the analyzer chamber 87To pump down the MSD 91

To move or store the MSD 93

To set the interface temperature from the GC 95





How to perform some basic operating procedures for the MSD.

CAUTIONThe software and firmware are revised periodically. If the steps in these procedures do

not match your MSD ChemStation software, refer to the manuals and online help

supplied with the software for more information.

Operating in Electron Impact (EI) Mode 3




Operating the MSD from the Data System

The software performs tasks such as pumping down, monitoring pressures,

setting temperatures, tuning, and preparing to vent. These tasks are described

in this chapter. Data acquisition and data analysis are described in the

manuals and online help supplied with the MSD ChemStation software.

Operating the MSD from the LCP

The local control panel (LCP) shows the status of the MSD or initiates a task

on the MSD without using the Agilent GC/MSD ChemStation.

The GC/MSD ChemStation may be located anywhere on the site local area

network (LAN), so the GC/MSD ChemStation might not be near the

instrument itself. And because the LCP communicates with the GC/MSD

ChemStation via the LAN, you can access GC/MSD ChemStation software

functions, such as tuning and starting a run, right from the MSD.

Modes of operation

The LCP has two modes of operation: Status and Menu.

Status mode requires no interaction and simply displays the current status of

the MSD instrument or its various communication connections. If you select

[Menu], then [No/Cancel], you will be returned to the Status mode.

Menu mode allows you to query various aspects of the GC/MSD and to initiate

some actions like running a method or sequence or preparing to vent the

system.

To access a particular menu option:

NOTEOnly certain functions are available from the LCP; the GC/MSD ChemStation is the

full-featured controller for most instrument control operations.

Press [Menu] until the desired menu appears.

Press [Item] until the desired menu item appears.





Use one or more of the following keys as appropriate to respond to prompts or

select options:

After you make your selection, or if you cycle through all available menus, the

display automatically returns to Status mode.

Pressing [Menu], then [No/Cancel], will always display the Status mode.

Pressing [No/Cancel] twice will always return to the Status mode.

Use [Up] to increase the displayed value or to scroll up (such as in a message list).

Use [Down] to decrease the displayed value or to scroll down (such as in a message

list).

Use [Yes/Select] to accept the current value.

Use [No/Cancel] to return to the Status mode.





LCP Status Messages

The following messages may be displayed on the LCP to inform you of the

status of the MSD system. If the LCP is currently in Menu mode, cycle through

the menus to return to Status mode.

ChemStation Loading <timestamp>

The Agilent MSD Productivity ChemStation software is starting up.

Executing <type>tune

A tuning procedure is in progress (type = QuickTune or Autotune).

Instrument Available <timestamp>

The Agilent MSD Productivity ChemStation software is not running.

Loading Method <method name>

Method parameters are being sent to the MSD.

Loading MSD FirmwareThe MSD’s firmware is being initialized.

The following messages alternately appear on the LCP if the MSD does NOT

complete its bootup sequence properly:

Server not Found

Check LAN Connection

Seeking Server

Bootp Query xxx

These messages indicate that the MSD has not received its unique IP address

from the Agilent Bootp Service. If the messages persist after you have logged

onto your account on the GC/MSD ChemStation, consult the Troubleshooting

section of the Software Installation manual.

NOTENo messages will be displayed if an online instrument session is not currently running on

the GC/MSD ChemStation.





Loading OS

The operating system of the instrument controller is being initialized.

<method> Complete <timestamp>

The run and subsequent data processing are done. The same message appears

even if the run was terminated prematurely.

Method Loaded <method name>Method parameters were sent to the MSD.

MS locked by <computer name>

MS parameters can only be changed from the GC/MSD ChemStation.

Press Sideplate

A reminder during startup to press the MSD sideplate to ensure an adequate

vacuum seal.

Run: <method> Acquiring <datafile>

A run is in progress; data is being acquired to the designated data file.

To view system status during startup

1 The following messages are displayed on the LCP display during startup:

• Press sideplate

• Loading OS

• Press sideplate

• Loading MSD Firmware

2 Continue to press the sideplate of the MSD until the MSD Ready message

appears. This helps the instrument to pump down more quickly.


LCP M




LCP Menus

To access a particular menu option, press [Menu] until the desired menu

appears, then press [Item] until the desired menu item appears. Table 6

through Table 11 list the menus and selections.

NOTEMany menu items, especially on the ChemStation, MS Parameters, and Maintenance

menus, have no effect when the instrument is acquiring data.

Table 6 ChemStation menu

Action Description

Run Method Displays the current method name and starts an analysis.

Run Sequence Displays the current sequence and starts a sequence.

Run Current Tune Displays the current tune file and starts an autotune (EI mode

only; CI tune must be started from the GC/MSD ChemStation).

# of Messages Displays the number of messages and the text of the most recent

message. Use the arrow keys to scroll through previous messages

(up to 20).

Release ChemStation Disassociates the GC/MSD ChemStation from the MSD.

Connection Status Displays the LAN connection status for the MSD.

Remote = connected to GC/MSD ChemStation online session

Local = not connected to GC/MSD ChemStation online session

Name of Instrument Displays the name of the instrument if connected to GC/MSD

ChemStation online session. The name of the instrument is the

name assigned to the MSD by the GC/MSD ChemStation

Configuration dialogue.


T bl 7 M i




Table 7 Maintenance menu

Action Description

Prepare to vent Reminds you to shut down the GC then prepares the instrument for

venting when [Yes/Select] is pressed.

Pumpdown Initiates a pumpdown sequence.

Table 8 MS Parameters menu

Action Description

High Vacuum Pressure Only with Micro-Ion vacuum gauge installed.

Turbo Pump Speed Displays the turbo pump speed.

Foreline Pressure Displays the foreline pressure.

MSD Fault Status Reports a summary fault status code (number) in ‘dec’ (decimal) and

‘hex’ (hexadecimal) format covering all possible fault combinations.

Ion Source Temp, oC Displays and sets the ion source temperature.

Mass Filter Temp, oC Displays and sets the mass filter temperature.

CI Reagent Displays CI reagent gas and flow rate (if installed).

NOTEMS parameters cannot be set from the LCP while an online GC/MSD ChemStation session

is connected to the MSD.

Table 9 Network menu

Action Description

MSD IP via BootP Displays the IP address for the MSD.

Gateway IP Address Displays the gateway IP address for the MSD.

Subnet Mask Displays the subnet mask for the MSD.

ChemStation IP Displays the IP address for the GC/MSD ChemStation.

GC IP Address Displays the IP address for the GC.

Ping gateway Checks communication with the gateway.


Table 9 Network menu (continued)




Ping ChemStation Checks communication with the GC/MSD ChemStation.

Ping GC Checks communication with the GC.

MS Controller MAC Displays the MAC address of the SmartCard in the MSD.

Table 10 Version menu

Action Description

Control firmware Displays the MSD firmware version.

Operating system Displays the GC/MSD ChemStation operating system version.

Front panel Displays the version of the LCP.

Log amplifier Displays version information.

Sideboard Displays the sideboard type.

Mainboard Displays the mainboard type.

Serial number Is assigned to the MSD by GC/MSD ChemStation Configuration

dialogue.

Table 11 Controller menu

Action Description

Reboot controller Starts the LAN/MS control card.

Test LCP? Initiates a diagnostic test of the two-line display.

Test HTTP link to GC/MSD

ChemStation?

Checks the status of the HTTP server.

Table 9 Network menu (continued)

Action Description


The EI GC/MSD Interface




The EI GC/MSD Interface

The GC/MSD interface (Figure 12) is a heated conduit into the MSD for the

capillary column. It is bolted onto the right side of the analyzer chamber, with

an O-ring seal. It has a protective cover which should be left in place.

One end of the GC/MSD interface passes through the side of the gas

chromatograph and extends into the GC oven. This end is threaded to allow

connection of the column with a nut and ferrule. The other end of the

interface fits into the ion source. The last 1 to 2 millimeters of the capillary column extend past the end of the guide tube and into the ionization chamber.

The GC/MSD interface is heated by an electric cartridge heater. Normally, the

heater is powered and controlled by Thermal Aux #2 heated zone of the GC.

For 6850 Series GCs, the heater is connected to the auxiliary thermal zone.

For the 7820A Series GC’s, the heater is either connected to the rear inlet

thermal zone for single inlet models or connected to the manual valve thermal

zone for dual inlet models. The interface temperature can be set from the MSDChemStation or from the gas chromatograph. A sensor (thermocouple) in the

interface monitors the temperature.

The GC/MSD interface should be operated in the 250 to 350 C range. Subject

to that restriction, the interface temperature should be slightly higher than the

maximum GC oven temperature, but never higher than the maximum column

temperature.

The EI GC/MSD interface can only be used with the EI ion source. However,the CI GC/MSD interface can be used with either source.

See Also

“To install a capillary column in the GC/MSD interface” .

WARNING The GC/MSD interface operates at high temperatures. If you touch it when it is hot,it will burn you.





Figure 12 The EI GC/MSD interface

Ionization

chamber

Analyzer

chamber

Heater/Sensor

assembly

MSD GC oven

Heater sleeve

Insulation

Column

Column end protrudes 1 to 2 mm into the ionization chamber.


Before You Turn On the MSD




Before You Turn On the MSD

Verify the following before you turn on or attempt to operate the MSD.

• The vent valve must be closed (the knob turned all the way clockwise).

• All other vacuum seals and fittings must be in place and fastened correctly.

(The the front side plate screw should not be tightened, unless hazardous

carrier or reagent gasses are being used.

• The MSD is connected to a grounded power source.

• The GC/MSD interface extends into the GC oven.

• A conditioned capillary column is installed in the GC inlet and in the

GC/MSD interface.

• The GC is on, but the heated zones for the GC/MSD interface, the GC inlet,

and the oven are off.

• Carrier gas of at least 99.9995% purity is plumbed to the GC with the

recommended traps.• If hydrogen is used as carrier gas, carrier gas f low must be off and the front

sideplate thumbscrew must be loosely fastened.

• The foreline pump exhaust is properly vented.

WARNINGThe exhaust from the foreline pump contains solvents and the chemicals you are

analyzing. If using the standard foreline pump, it also contains traces of pump oil. If

you are using toxic solvents or analyzing toxic chemicals, remove the oil trap(standard pump) and install a hose (11-mm id) to take the foreline pump exhaust

outside or to a fume (exhaust) hood. Be sure to comply with local regulations. The

oil trap supplied with the standard pump stops only pump oil. It does not trap or filter

out toxic chemicals.


MSD has been pumped down. If the vacuum pumps are off, hydrogen will

accumulate in the MSD and an explosion may occur. Read “Hydrogen Safety”

before operating the MSD with hydrogen carrier gas.


Pumping Down

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p g

The data system or local control panel helps you pump down the MSD. The

process is mostly automated. Once you close the vent valve and turn on the

main power switch (while pressing on the sideplate), the MSD pumps down by

itself. The data system software monitors and displays system status during

pumpdown. When the pressure is low enough, the program turns on the ion

source and mass filter heaters and prompts you to turn on the GC/MSD

interface heater. The MSD will shut down if it cannot pump down correctly.

Using the menus or MS monitors, the data system can display:

• Motor speed for turbo pump MSDs (percent spin speed)

• Foreline pressure for diffusion pump MSDs

• Analyzer chamber pressure (vacuum) for MSDs with the optional G3397A

Micro-Ion Gauge Controller

The LCP can also display these data.

Controlling Temperatures

MSD temperatures are controlled through the data system. The MSD has

independent heaters and temperature sensors for the ion source and

quadrupole mass filter. You can adjust the setpoints and view these

temperatures from the data system or from the local control panel.

Normally, the GC/MSD interface heater is powered and controlled by the

Thermal Aux #2 heated zone of the GC. For the 6850 Series GCs, the heater is

connected to the auxiliary thermal zone. For the 7820 Series GCs, the heater is

either connected to the rear inlet thermal zone for single inlet models or is

connected to the manual valve thermal zone for dual inlet models. The

GC/MSD interface temperature can be set and monitored from the data

system or from the GC.


Controlling Column Flow




g

Carrier gas flow is controlled by head pressure in the GC. For a given head

pressure, column flow will decrease as the GC oven temperature increases.

With electronic pneumatic control (EPC) and the column mode set to Constant

Flow, the same column flow is maintained regardless of temperature.

The MSD can be used to measure actual column flow. You inject a small

amount of air or other unretained chemical and time how long it takes to

reach the MSD. With this time measurement, you can calculate the columnflow. See page 73.


Venting the MSD




A program in the data system guides you through the venting process. It turns

off the GC and MSD heaters and diffusion pump heater or the turbo pump at

the correct time. It also lets you monitor temperatures in the MSD and

indicates when to vent the MSD.

The MSD will be damaged by incorrect venting. A diffusion pump will

backstream vaporized pump fluid onto the analyzer if the MDS is vented

before the diffusion pump has fully cooled. A turbo pump will be damaged if it is vented while spinning at more than 50% of its normal operating speed.

WARNINGMake sure the GC/MSD interface and the analyzer zones are cool (below 100 °C)

before you vent the MSD. A temperature of 100 °C is hot enough to burn skin; always

wear cloth gloves when handling analyzer parts.

WARNINGIf you are using hydrogen as a carrier gas, the carrier gas flow must be off before

turning off the MSD power. If the foreline pump is off, hydrogen will accumulate in

the MSD and an explosion may occur. Read “Hydrogen Safety” before operating

the MSD with hydrogen carrier gas.

CAUTION Never vent the MSD by allowing air in through either end of the foreline hose. Use thevent valve or remove the column nut and column.

Do not vent while the turbo pump is still spinning at more than 50%.

Do not exceed the maximum recommended total gas flow. See “5975 series MSD

models and features” .


To view MSD analyzer temperature and vacuum status




You can also use the Local Control Panel to perform this task. See the

G1701EA GC/MSD ChemStation Getting Started manual for more

information.

Procedure

1 In Instrument Control view, select Edit Tune Parameters from the Instrument

menu (Figure 13).

2 Select the tune file you plan to use with your method from the Load MS Tune

File dialog box.

3 Analyzer temperatures and vacuum status are displayed in the Zones field.

Figure 13 Tune parameters


Unless you have just begun the pumpdown process, the foreline pressure

should be less than 300 mTorr or the turbo pump should be running at least




should be less than 300 mTorr, or the turbo pump should be running at least

80% speed. MSD heaters remain off as long as the diffusion pump is cold or theturbo pump is operating at less than 80%. Normally, the foreline pressure will

be below 100 mTorr, or the turbo pump speed will be at 100%.

The MSD heaters turn on at the end of the pumpdown cycle and turn off at the

beginning of the vent cycle. The reported setpoints will not change during

venting or pumpdown, even though both the MSD zones are turned off.


To set monitors for MSD temperature and vacuum status




A monitor displays the current value of a single instrument parameter. They

can be added to the standard instrument control window. Monitors can be set

to change color if the actual parameter varies beyond a user-determined limit

from its setpoint.

Procedure

1 Select MS Monitors from the Instrument menu.

2 In the Edit MS Monitors box, under Type, select Zone.3 Under Parameter, select MS Source and click Add.

4 Under Parameter, select MS Quad and click Add.

5 Under Parameter, select Foreline (or TurboSpd) and click Add.

6 Select any other monitors you want and Add them.

7 Click OK. The new monitors will be stacked on top of each other in the lower

right corner of the Instrument Control window. They must be moved for youto see them all.

8 Click and drag each monitor to the desired position. See Figure 14 for one

way of arranging the monitors.

9 To make the new settings part of the method, select Save from the Method

menu.

Figure 14 Arranging monitors


To set the MSD analyzer temperatures




Setpoints for the MSD ion source and mass filter (quad) temperatures are

stored in the current tune (*.u) file. When a method is loaded, the setpoints in

the tune file associated with that method are downloaded automatically.

Procedure

1 In Instrument Control view, select Edit Tune Parameters from the Instrument

menu.2 Select Temperatures from the MoreParams menu (Figure 15).

3 Type the desired Source and Quad (mass filter) temperatures in the

setpoint fields. See Table 12 for recommended setpoints.

The GC/MSD interface, ion source, and quadrupole heated zones interact.

The analyzer heaters may not be able to accurately control temperatures if

the setpoint for one zone is much different from that of an adjacent zone.

Figure 15 Setting temperatures

WARNINGDo not exceed 200 °C for the quadrupole or 350 °C for the source.


4 To close the screen, click:




• Apply to send the new temperature setpoints to the MSD.• OK to change the currently loaded tune file but not download anything to

the MSD (use Apply).

• Cancel to exit the panel without changing the currently loaded tune file

or downloading anything to the MSD.

5 When the Save MS Tune File dialog box appears, either click OK to save your

changes to the same file or type a new file name and click OK.

Table 12 Recommended temperature settings

EI operation PCI operation NCI operation

MS Source 230 250 150

MS Quad 150 150 150


To set the GC/MSD interface temperature from the ChemStation




You can also use the Local Control Panel to perform this task. See “Operating

the MSD from the LCP” .

Procedure

1 Select View>Instrument Control.

2 Select Instrument>GC Edit Parameters.

3 Click the Aux icon to edit the interface temperature (Figure 16).

4 Check the heater On and type the setpoint in the Value °C column.

The typical setpoint is 280 °C. The limits are 0 °C and 350 °C. A setpoint

below ambient temperature turns off the interface heater.

Figure 16 Setting the interface temperature


CAUTION

Never exceed the maximum temperature for your column.




5 Click Apply to download setpoints or click OK to download setpoints and

close the window.

6 To make the new settings part of the method, select Save from the Method

menu.

CAUTION

CAUTIONMake sure that the carrier gas is turned on and the column has been purged of air

before heating the GC/MSD interface or the GC oven.


To monitor high vacuum pressure




Pressure monitoring requires an optional G3397A Micro-Ion vacuum gauge.

Materials needed

• Micro-Ion vacuum gauge (G3397A)

Procedure

1 Start up and pump down the MSD (page 91).

2 In the Tune and Vacuum Control view select Turn Vacuum Gauge on/off from

the Vacuum menu.

3 In the Instrument Control view you can set up an MS Monitor for reading.

The vacuum can also be read on the LCP or from the Manual Tune screen.

The largest influence on operating pressure in EI mode is the carrier gas

(column) flow. Table 13 lists typical pressures for various helium carrier gas

flows. These pressures are approximate and will vary from instrument toinstrument by as much as 30%.

WARNINGIf you are using hydrogen as a carrier gas, do not turn on the Micro-Ion vacuum

gauge if there is any possibility that hydrogen has accumulated in the analyzer

chamber. Read “Hydrogen Safety” before operating the MSD with hydrogen carrier

gas.


Table 13 Micro-Ion Vacuum Gauge Reading




If the pressure is consistently higher than those listed, refer to the online help

in the MSD ChemStation software for information on troubleshooting air leaks

and other vacuum problems.

Column flow rate,

mL/min

Gauge reading, Torr

Performance turbo

pump

Gauge reading, Torr

Standard turbo

pump

Gauge reading, Torr

Diffusion pump

Foreline reading, Torr

Diffusion pump

0.5 3.18E–06 1.3E–05 2.18E–05 34.7

0.7 4.42E–06 1.83E–05 2.59E–05 39.4

1 6.26E–06 2.61E–05 3.66E–05 52.86

1.2 7.33E–06 3.11E–05 4.46E–05 60.866

2 1.24E–05 5.25E–05 7.33E–05 91.784

3 1.86E–05 8.01E–05 1.13E–04 125.76

4 2.48E–05

6 3.75E–05


To measure column flow linear velocity




With capillary columns, such as those used with the MSD, linear velocity is

often measured rather than volumetric flow rate.

Procedure

1 Set Data Acquisition for splitless manual injection and selected ion

monitoring (SIM) of m/z 28.

2 Press Prep Run on the GC keypad.

3 Inject 1 µL of air into the GC inlet and press Start Run.

4 Wait until a peak elutes at m/z 28. Note the retention time.

5 Calculate the average linear velocity.

Average linear velocity (cm/s) =

where:

L = Length of the column in meters

t = Retention time in seconds

Be sure to account for any pieces of column broken off. A 1-meter section

missing from a 25-meter column can yield a 4% error.

6 Use this velocity to verify the MSD ChemStation flow calculations (page 74).

If the numbers disagree, click Change to calibrate the column dimensions.

7 To calculate the volumetric flow rate.

Volumetric flow rate (mL/min) =

where:

D = Internal column diameter in millimeters

L = Column length in meters

t = Retention time in minutes

100 L

t --------------

0.785 D2 L

t

----------------------------


To confirm column flow




Volumetric flow can be calculated from the column head pressure if the

column dimensions are known.

Procedure

1 In the Instrument Control view, select Instrument>GC Edit Parameters.

2 Click the Columns icon (Figure 17 shows an example).

3 Select the appropriate column. .

Figure 17 Calculating column flow


To tune the MSD

Y l h L l C l P l h h i l




You can also use the Local Control Panel to run the autotune that is currently

loaded in the PC memory. See “Operating the MSD from the LCP” .

Procedure

1 In the Instrument Control View, verify the correct tune file is loaded. For

most applications, ATUNE.U (Autotune) gives good results. STUNE.U

(Standard Tune) is not recommended as it may reduce sensitivity.Consider Gain autotune (GAIN.U + HiSense.U). This tunes to a target gain

rather than a target abundance. It offers excellent reproducibility, both of

run-to-run abundance but also between different instruments,

2 Set the system to the same conditions (GC oven temperature and column

flow, and MSD analyzer temperatures) that will be used for data

acquisition.

3 Select Tune MSD to perform a complete tune, or select Quick Tune to adjust peak width, mass assignment, and abundance, without changing ion ratios.

If your system is configured for CI, you will be able to access the CI Tune

panel from this box. The tune will start immediately.

4 Wait for the tune to complete and to generate the report.

Save your tune reports. To view history of tune results, select

Checkout>View Previous Tunes....

To manually tune your MSD or to perform special autotunes, go to the Tune

and Vacuum Control View.

From this Tune menu, in addition to the tunes available from Instrument

Control, you can select special autotunes for specific spectral results, such as

DFTPP Tune or BFB Tune.

See the manuals or online help provided with your MSD ChemStation software

for additional information about tuning.


To verify system performance

Materials needed




Materials needed

• 1 pg/µL (0.001 ppm) OFN sample (5188-5348)

Verify the tune performance

1 Verify that the system has been pumping down for at least 60 minutes.

2 Set the GC oven temperature to 150 °C and the column flow to 1.0 mL/min.3 In the Instrument Control view, select Checkout Tune from the Checkout

menu. The software will perform an autotune and print the report.

4 When the autotune has completed, save the method and then select

Evaluate Tune from the Checkout menu.

The software will evaluate the last autotune and print a System Verification

– Tune report.

Verify the sensitivity performance

1 Set up to inject 1 µL of OFN, either with the ALS or manually.

2 In the Instrument Control view, select Sensitivity Check from the Checkout

menu.

3 Click the appropriate icons in the Instrument Edit window to edit the

method for the type of injection.

4 Click OK to run the method.

When the method is completed, an evaluation report will be printed.

Verify that rms signal-to-noise ratio meets the published specification.

Please see the Agilent Web site at www.agilent.com/chem for specifications.


High-Mass Testing (5975 Series MSDs)

Setup conditions




Setup conditions

1 Obtain a sample of PFHT (5188-5357).

2 Load tune file ATUNE.U then auto tune the MSD.

3 Resolve the PFHT.M method under x\5975\PFHT.M where x is instrument

number being used.

4 Update and save the method.

High-mass checkout

1 Load sample into a vial and place in position 2.

2 Select High Mass Check from the Checkout menu.

3 Follow the instructions on screen.

4 The Run is completed and results are printed within 5 minutes.


Results




Figure 18 PFHT high mass report


Results will indicate the recommended amount to adjust AMU offset for

high-mass. If your results are within 5 units of the targeted amount, there is no

need to make adjustments.




Adjustments

1 Verify ATUNE.U has been loaded.

2 Select Edit Tune Parameters from the Instrument menu via Instrument

Control.

3 Click on MoreParams and select DynamicRamping Params...

a Select AMU offset from the drop down box.

b If the values on the right side are greyed out then select the Enable

Dynamic Ramping For This Lens checkbox.

c Enter in the recommend offset and click OK.

4 Click OK on the Edit Parameters box. The Save MS Tune File dialog box

appears.

You can overwrite the existing ATUNE.U to include high-mass adjustment

or save this file to a new name, for example, ATUNEHIGH.U.

5 Load the PFHT.M and the saved tune file, then save the method.

6 Rerun test mixture (repeat high-mass checkout). If the correction is within

5 units, no further adjustments are required.

NOTEAnytime an ATUNE.U is performed it will overwrite the AMU offset which was entered. This

is the reason for renaming the tune.


To remove the MSD covers

Materials needed




• Screwdriver, Torx T-15 (8710-1622)

If you need to remove one of the MSD covers, follow these procedures

(Figure 19):

To remove the analyzer top cover

Remove the five screws and lift the cover off.

To remove the analyzer window cover

1 Press down on the rounded area on the top of the window.

2 Lift the window forward and off the MSD.

WARNINGDo not remove any other covers. Dangerous voltages are present under other covers.


Analyzer window cover

http://localhost/var/www/apps/conversion/tmp/Videos/RemoveEItopcover.wmv


http://localhost/var/www/apps/conversion/tmp/Videos/Removefrontcover.wmv







Figure 19 Removing covers

Latch

Analyzer cover

Left side cover

CAUTION Do not use excessive force or the plastic tabs that hold the cover to the mainframe willbreak off.


To vent the MSD

Procedure




1 Select Vent from the Vacuum menu in the software. Follow the instructions

presented.

2 Set the GC/MSD interface heater and the GC oven temperatures to ambient

(room temperature).

3 When prompted, turn off the MSD power switch.

4 Unplug the MSD power cord.

WARNINGIf you are using hydrogen as a carrier gas, the carrier gas flow must be off before

turning off the MSD power. If the foreline pump is off, hydrogen will accumulate in

the MSD and an explosion may occur. Read “Hydrogen Safety” before operating

the MSD with hydrogen carrier gas.

CAUTION Be sure the GC oven and the GC/MSD interface are cool before turning off carrier gasflow.

WARNINGWhen the MSD is vented, do not put the ChemStation into Instrument Control view.

Doing so will turn on the interface heater.


5 Remove the analyzer window cover (page 80)




6 Turn the vent valve knob (Figure 20) counterclockwise only 3/4 turns or

until you hear the hissing sound of air flowing into the analyzer chamber.

Do not turn the knob too far or the O-ring may fall out of its groove. Be sure

to retighten the knob before pumping down.

Figure 20 Venting the MSD

Vent valve knob YES NO

WARNINGAllow the analyzer to cool to near room temperature before touching it.

CAUTION Always wear clean gloves while handling any parts that go inside the analyzerchamber.

WARNINGWhen the MSD is vented, do not put the ChemStation into Instrument Control view.

Doing so will turn on the interface heater.


To open the analyzer chamber

Materials needed

http://localhost/var/www/apps/conversion/tmp/Videos/VenttheMSD.wmv






• Gloves, clean, lint-free

• Large (8650-0030)

• Small (8650-0029)

• Wrist strap, antistatic

• Small (9300-0969)• Medium (9300-1257)

• Large (9300-0970)

Procedure

1 Vent the MSD (page 82).

2 Disconnect the side board control cable and the source power cable from

the side board.

3 Loosen the side plate thumbscrews (Figure 21) if they are fastened.

The rear side plate thumbscrew should be unfastened during normal use. It

is only fastened during shipping. The front side plate thumbscrew should

only be fastened for CI operation or if hydrogen or other flammable or toxic

substances are used for carrier gas.

4 Gently swing the side plate out.

CAUTIONElectrostatic discharges to analyzer components are conducted to the side board

where they can damage sensitive components. Wear a grounded antistatic wrist strap

and take other antistatic precautions (see page 131) before you open the analyzer

chamber.

CAUTION In the next step, if you feel resistance, stop. Do not try to force the side plate open.Verify that MSD is vented. Verify that both the front and rear side plate screws are

completely loose.


WARNINGThe analyzer, GC/MSD interface, and other components in the analyzer chamber

operate at very high temperatures. Do not touch any part until you are sure it is cool.

http://localhost/var/www/apps/conversion/tmp/Videos/openAnalyzer.wmv






CAUTIONAlways wear clean gloves to prevent contamination when working in the analyzer

chamber.


Thumbscrews




Figure 21 The analyzer chamber

Side plate

Analyzer cover

Detector

Feedthrough board

Ion source

Analyzer

Side plate

CHAMBER CLOSED

CHAMBER OPEN


To close the analyzer chamber

Materials needed

Gl l li f





• Large (8650-0030)

• Small (8650-0029)

Procedure

1 Make sure all the internal analyzer electrical leads are correctly attached.

Wiring is the same for both the EI and CI sources.

The wiring is described in Table 14 and illustrated in Figure 22 and

Figure 23. The term “Board” in the table refers to the feedthrough board

located next to the ion source.

Table 14 Analyzer wiring

Wire description Attached to Connects to

Green beaded (2) Quad heater Board, top left (HTR)

White with braided cover (2) Quad sensor Board, top (RTD)

White (2) Board, center (FILAMENT-1) Filament 1 (top)

Red (1) Board, center left (REP) Repeller

Black (2) Board, center (FILAMENT-2) Filament 2 (bottom)

Orange (1) Board, top right (ION FOC) Ion focus lens

Blue (1) Board, top right (ENT LENS) Entrance lens

Green beaded (2) Ion source heater Board, bottom left (HTR)

White (2) Ion source sensor Board, bottom (RTD)


HTR

QUADRUPOLE




Figure 22 Feedthrough board wiring

HTRRTS

SOURCE

FILAMENT - 2

FILAMENT - 1

REP

IONFOC

ENTRLENS

RTS

White wires to

filament 1

Red wire

to repeller

Black wires to

filament 2

Ion source heater

wires (green)

Blue wire to

entrance lens

Orange wire to

ion focus lens

Ion source sensor

wires (white)


FB = Feedthrough Board

Repeller




2 Check the side plate O-ring.

Make sure the O-ring has a very light coat of Apiezon L high vacuum grease.

If the O-ring is very dry, it may not seal well. If the O-ring looks shiny, it has

too much grease on it. (Refer to the 5975 Series MSD Troubleshooting and

Maintenance Manual for lubricating instructions.)

Figure 23 Ion source wiring

Ion source

heater wires

Ion source

sensor wires

p

(red wire

from FB)

Filament 1

(white wires

from FB)

Filament 2

(black wires

from FB)

Ion focus lens

(orange wire

from FB)

Entrance lens

(blue wire

from FB)


3 Close the side plate.

4 Reconnect the side board control cable and source power cable to the side

board.

5 Make sure the vent valve is closed.




6 Pump down the MSD (page 91).

7 If you are operating in CI mode or if hydrogen or other flammable or toxic

substance is used for carrier gas, gently hand tighten the front side plate

thumbscrew.

8 Once the MSD has pumped down, close the analyzer cover.

WARNINGThe front thumbscrew must be fastened for CI operation or if hydrogen (or other

hazardous gas) is being used as the GC carrier gas. In the unlikely event of an

explosion, it may prevent the side plate from opening.

CAUTIONDo not overtighten the thumbscrew; it can cause air leaks or prevent successful

pumpdown. Do not use a screwdriver to tighten the thumbscrew.


To pump down the MSD

You can also use the Local Control Panel to perform this task. See “Operating

the MSD from the LCP” .




Procedure

1 Close the vent valve.

2 Plug in the MSD power cord.

3 Open the MSD Analyzer top cover.

4 Turn on the MSD while engaging the side plate to the manifold using hand

pressure.

5 Press lightly on the side board to ensure a correct seal. Press on the metal

box on the side board.

The foreline pump will make a gurgling noise. This noise should stop within

a minute. If the noise continues, there is a large air leak in your system,

probably at the side plate seal, the interface column nut, or the vent valve.

6 Start the ChemStation and select Tune and Vacuum Control from the View

menu.

7 Select Pump Down from the Vacuum menu.

WARNINGMake sure your MSD meets all the conditions listed in the introduction to this

chapter (page 60) before starting up and pumping down the MSD. Failure to do so

can result in personal injury.


MSD has been pumped down. If the vacuum pumps are off, hydrogen will

accumulate in the MSD and an explosion may occur. Read “Hydrogen Safety”

before operating the MSD with hydrogen carrier gas.


8 Once communication with the PC has been established, click OK.

http://localhost/var/www/apps/conversion/tmp/Videos/PumpdownMSD.wmv






9 When prompted, turn on the GC/MSD interface heater and GC oven. Click

OK when you have done so.

The software will turn on the ion source and mass filter (quad) heaters. The

temperature setpoints are stored in the current autotune (*.u) file.

10 After the message Okay to run appears, wait 2 hours for the MSD to reach

thermal equilibrium. Data acquired before the MSD has reached thermal

equilibrium may not be reproducible.

Figure 24 Pumping down

CAUTIONWithin 10 to 15 minutes the diffusion pump should be hot, or the turbo pump speed

should be up to 80% (Figure 24). The pump speed should eventually reach 95%. If these

conditions are not met, the MSD electronics will shut off the foreline pump. In order torecover from this condition, you must power cycle the MSD. If the MSD does not pump

down correctly, see the manual or online help for information on troubleshooting air

leaks and other vacuum problems.

CAUTIONDo not turn on any GC heated zones until carrier gas flow is on. Heating a column with

no carrier gas flow will damage the column.


To move or store the MSD

Materials needed

• Ferrule, blank (5181-3308)




• Interface column nut (05988-20066)

• Wrench, open-end, 1/4-inch × 5/16-inch (8710-0510)

Procedure

1 Vent the MSD (page 82).

2 Remove the column and install a blank ferrule and interface nut.

3 Tighten the vent valve.

4 Move the MSD away from the GC (see the 5975 Series MSD Troubleshooting

and Maintenance Manual).

5 Unplug the GC/MSD interface heater cable from the GC.

6 Install the interface nut with the blank ferrule.

7 Open the analyzer cover (page 80).

8 Finger-tighten the side plate thumbscrews (Figure 25).

9 Plug the MSD power cord in.

10 Switch the MSD on to establish a rough vacuum. Verify that the turbo pump

speed is greater than 50% or that the foreline pressure is 1 Torr.

11 Switch the MSD off.

12Close the analyzer cover.

13 Disconnect the LAN, remote, and power cables.

CAUTIONDo not overtighten the side plate thumbscrews. Overtightening will strip the threads in

the analyzer chamber. It will also warp the side plate and cause leaks.


Front thumbscrew




The MSD can now be stored or moved. The foreline pump cannot be

disconnected; it must be moved with the MSD. Make sure the MSD remains

upright and is never tipped on its side or inverted.

Figure 25 Side plate thumbscrews

Rear thumbscrew

CAUTION The MSD must remain upright at all times. If you need to ship your MSD to anotherlocation, contact your Agilent Technologies service representative for advice about

packing and shipping.


To set the interface temperature from the GC

If desired, the interface temperature can be set directly at the GC. For the

Agilent 7890A and 6890, set the Aux #2 temperature. For the 6850, use the

optional handheld controller to set the thermal aux temperature. Refer to the




GC User documentation for details.

If you want the new setpoint to become part of the current method, click Save under the Method menu. Otherwise, the first time a method is loaded, all the

setpoints in the method will overwrite those set from the GC keyboard.

CAUTIONNever exceed the maximum temperature of your column.

CAUTIONMake sure that the carrier gas is turned on and the column has been purged of air

before heating the GC/MSD interface or the GC oven.






Operation Manual

4Operating in Chemical Ionization (CI)

Mode




Mode

General Guidelines 98

The CI GC/MSD Interface 99

To Operate the CI MSD 101To switch from the EI source to the CI source 102

To pump down the CI MSD 103

To set up the software for CI operation 104

To operate the reagent gas flow control module 106

To set up methane reagent gas flow 109

To use other reagent gases 111

To switch from the CI source to the EI source 115

CI Autotune 116

To perform a PCI autotune (methane only) 118

To perform an NCI autotune (methane reagent gas) 120

To verify PCI performance 122

To verify NCI performance 123


This chapter provides information and instructions for operating the

5975 Series CI MSDs in Chemical Ionization (CI) mode. Most of the

information in the preceding chapter is also relevant.

Most of the material is related to methane chemical ionization but one sectiondiscusses the use of other reagent gases.

The software contains instructions for setting the reagent gas flow and for

performing CI autotunes. Autotunes are provided for positive CI (PCI) with

methane reagent gas and for negative CI (NCI) with any reagent gas.


General Guidelines

• Always use the highest purity methane (and other reagent gases, if

applicable.) Methane must be at least 99.9995% pure.

• Always verify the MSD is performing well in EI mode before switching to CI.




See “To verify system performance” .

• Make sure the CI ion source and GC/MSD interface tip seal are installed.

• Make sure the reagent gas plumbing has no air leaks. This is determined in

PCI mode, checking for m/z 32 after the methane pretune.

Operating in Chemical Ionization (CI) Mode 4

The CI GC/MSD Interface

The CI GC/MSD interface (Figure 26) is a heated conduit into the MSD for the

capillary column. It is bolted onto the right side of the analyzer chamber, with

an O-ring seal and has a protective cover which should be left in place.




One end of the interface passes through the side of the GC and extends into

the oven. It is threaded to allow connection of the column with a nut and

ferrule. The other end of the interface fits into the ion source. The last 1 to

2 millimeters of the capillary column extend past the end of the guide tube

and into the ionization chamber.

Reagent gas is plumbed into the interface. The tip of the interface assembly

extends into the ionization chamber. A spring-loaded seal keeps reagent gases

from leaking out around the tip. The reagent gas enters the interface body and

mixes with carrier gas and sample in the ion source.

The GC/MSD interface is heated by an electric cartridge heater. Normally, the

heater is powered and controlled by Thermal Aux #2 heated zone of the GC.

For 6850 Series GCs, the heater is connected to the auxiliary thermal zone.

The interface temperature can be set from the MSD ChemStation or from the

gas chromatograph. A sensor (thermocouple) in the interface monitors the

temperature.

This interface is also used for EI operation in CI MSDs.

The interface should be operated in the 250 to 350 C range. Subject to that

restriction, the interface temperature should be slightly higher than themaximum GC oven temperature, but never higher than the maximum column

temperature.

See Also

“To install a capillary column in the GC/MSD interface” .

CAUTIONNever exceed the maximum column temperature, either in the GC/MSD interface, the

GC oven, or the inlet.


WARNINGThe GC/MSD interface operates at high temperatures. If you touch it when it is hot,

it will burn you.




Figure 26 The CI GC/MSD interface

Spring-loadedseal

Reagent gas in

MSD GC oven

Column end protrudes 1 to 2 mm into the ionization chamber.


To Operate the CI MSD

Operating your MSD in the CI mode is slightly more complicated than

operating in the EI mode. After tuning, gas flow, source temperature

(Table 15), and electron energy may need to be optimized for your specific

analyte.




y

Start the system in PCI mode

By bringing the system up in PCI mode first, you will be able to do the

following:

• Set up the MSD with methane first, even if you are going to use another

reagent gas.

• Check the interface tip seal by looking at the m/z 28 to 27 ratio (in the

methane flow adjust panel).

• Tell if a gross air leak is present by monitoring the ions at m/z 19

(protonated water) and 32.

• Confirm that the MS is generating “real” ions and not just background

noise.

It is nearly impossible to perform any diagnostics on the system in NCI. In

NCI, there are no reagent gas ions to monitor. It is difficult to diagnose an air

leak and difficult to tell whether a good seal is being created between the

interface and the ion volume.

Table 15 Temperatures for CI operation

Ion source Quadrupole GC/MSDinterface

PCI 250 °C 150 °C 280 °C

NCI 150 °C 150 °C 280 °C


To switch from the EI source to the CI source

CAUTIONAlways verify MSD performance in EI before switching to CI operation.

Always set up the CI MSD in PCI first, even if you are going to run NCI.




Procedure

1 Vent the MSD. See page 82.2 Open the analyzer.

3 Remove the EI ion source. See page 134.

4 Install the CI ion source. See page 142.

5 Install the interface tip seal. See page 143.

6 Close the analyzer.

7 Pump down the MSD. See page 103.


where they can damage sensitive components. Wear a grounded antistatic wrist strap.

See “Electrostatic discharge” . Take antistatic precautions before you open the

analyzer chamber.


To pump down the CI MSD

You can also use the Local Control Panel to perform this task. See “Operatingthe MSD from the LCP” .

Procedure




1 Follow the instructions for the EI MSD. See “To pump down the MSD” .

After the software prompts you to turn on the interface heater and GC

oven, perform the following steps.2 Check the vacuum gauge, if present, to verify that the pressure is

decreasing.

3 Press Shutoff Valve to close the gas supply and shutoff valves.

4 Verify that PCICH4.U is loaded and accept the temperature setpoints.

Always start up and verify system performance in PCI mode before

switching to NCI.

5 Set the GC/MSD interface to 280 °C.

6 Set Gas A to 20%.

7 Let the system bake out and purge for at least 2 hours. If you will be

running NCI, best sensitivity, bake out the MSD overnight.


To set up the software for CI operation

Procedure

1 Switch to the Tune and Vacuum Control view.

2 Select Load Tune Values from the File menu.




3 Select the tune file PCICH4.U.

4 If CI autotune has never been run for this tune file, the software will

prompt you through a series of dialog boxes. Accept the default values

unless you have a very good reason for changing anything.

The tune values have a dramatic effect on MSD performance. Always start

with the default values when first setting up for CI, and then make

adjustments for your specific application. See Table 16 for default values

for the Tune Control Limits box.

NOTEThese limits are used by Autotune only. They should not be confused with the parameters

set in Edit MS Parameters or with those appearing on the tune report.


Table 16 Default Tune Control Limits, used by CI autotune only

Reagent gas Methane Isobutane Ammonia

Ion polarity Positive Negative Positive Negative Positive Negative

Abundance target 1x106 1x106 N/A 1x106 N/A 1x106




Notes for Table 16:

• N/A Not available. There are no PFDTD ions formed in PCI with any

reagent gas but methane, hence, CI autotune is not available with theseconfigurations.

• Ion polarity Always set up in PCI with methane first, then switch to your

desired ion polarity and reagent gas.

• Abundance target Adjust higher or lower to get desired signal abundance.

Higher signal abundance also gives higher noise abundance. This is

adjusted for data acquisition by setting the EMV in the method.

• Peakwidth target Higher peakwidth values give better sensitivity, lower values give better resolution.

• Maximum emission current Optimum emission current maximum for NCI

is very compound-specific and must be selected empirically. Optimum

emission current for pesticides, for example, may be about 200 µA.

Peakwidth target 0.6 0.6 N/A 0.6 N/A 0.6

Maximum repeller 4 4 N/A 4 N/A 4

Maximum emissioncurrent, µA

240 50 N/A 50 N/A 50

Max electron energy, eV 240 240 N/A 240 N/A 240


To operate the reagent gas flow control module

Reagent gas flows are controlled in software (Figure 27).




The Valve Settings have the following effects:

Gas A (or B) Valve The present gas flow, if any, is turned off. The system

evacuates the gas lines for 6 minutes, then turns on the selected gas (A or B).

This is to reduce cross-mixing of the gases in the lines.

Shutoff Valve When Shutoff Valve is selected, the system turns off the present

gas flow while leaving the shutoff valve (Figure 28) open. This is to remove any

residual gas in the lines. Typical evacuation time is 6 minutes and then the

shutoff valve is closed.

The flow control hardware remembers the flow setting for each gas. When

either gas is selected, the control board automatically sets the same flow that

was used for that gas last time.

Figure 27 CI flow control


The flow control module

The CI reagent gas flow control module (Figure 28 and Table 17) regulates the

flow of reagent gas into the CI GC/MSD interface. The flow module consists of a mass flow controller (MFC), gas select valves, CI calibration valve, shutoff

valve, control electronics, and plumbing.

The back panel provides Swagelok inlet fittings for methane (CH4) and one




OTHER reagent gas. The software refers to them as Gas A and Gas B,

respectively. If you are not using a second reagent gas, cap the OTHER fitting to

prevent accidental admission of air to the analyzer. Supply reagent gases at

25 to 30 psi (170 to 205 kPa).

The shutoff valve prevents contamination of the flow control module by

atmosphere while the MSD is vented or by PFTBA during EI operation. The

MSD monitors will reflect On as 1 and Off as 0 (see Table 17).

Figure 28 Reagent gas flow control module schematic

Gas A

(methane)

supply

Gas B

(other)

supply

Gas A

select valve

Gas B

select valve

Mass

flowcontroller

Calibration

valve

Restrictor

Calibration

vial

Shutoff

valve

GC/MSD

interface

GC column

CI ion

source


Table 17 Flow control module state diagram

Result Gas A flow Gas B flow Purge

with Gas A

Purge

with Gas B

Pump out

flow module

Standby,

vented, or EI

mode

Gas A Open Closed Open Closed Closed Closed




The Open and Closed states are shown in the monitors as 1 and 0 respectively.

Gas B Closed Open Closed Open Closed Closed

MFC On setpoint On setpoint On 100% On 100% On 100% Off 0%

Shutoff valve Open Open Open Open Open Closed


To set up methane reagent gas flow

The reagent gas flow must be adjusted for maximum stability before tuning theCI system. Do the initial setup with methane in positive chemical ionization

(PCI) mode. No flow adjustment procedure is available for NCI, as no negative

reagent ions are formed.

Adj ti th th t fl i th t tti th




Adjusting the methane reagent gas flow is a three-step process: setting the

flow control, pretuning on the reagent gas ions, and adjusting the flow for

stable reagent ion ratios, for methane, m/z 28/27.

Your data system will prompt you through the flow adjustment procedure.

Procedure

1 Select Gas A. Follow the instructions and prompts from the Tune Wizard.

2 Set the flow to 20% for PCI/NCI MSDs.

3 Check the vacuum gauge controller to verify correct pressure. See page 124.

4 Select Methane Pretune from the Setup menu.

The methane pretune tunes the instrument for optimum monitoring of the

ratio of methane reagent ions m/z 28/27.

5 Examine the displayed profile scan of the reagent ions (Figure 29).

• Make sure there is no visible peak at m/z 32. A peak there indicates an

air leak. If such a peak is present, find and repair the leak before

proceeding. Operating in the CI mode with an air leak will rapidly

contaminate the ion source.

• Make sure that the peak at m/z 19 (protonated water) is less than 50% of

the peak at m/z 17.

6 Perform the Methane Flow Adjust.

CAUTIONAfter the system has been switched from EI to CI mode, or vented for any other reason,

the MSD must be baked out for at least 2 hours before tuning.


CAUTIONContinuing with CI autotune if the MSD has an air leak or large amounts of water will

result in severe ion source contamination. If this happens, you will need to vent the

MSD and clean the ion source .




Methane pretune after more than a day of baking out

Note the low abundance of m/z 19 and absence of any visible peak at m/z 32.

Your MSD will probably show more water at first, but the abundance of m/z 19

should still be less than 50% of m/z 17.

Figure 29 Reagent ion scans


To use other reagent gases

This section describes the use of isobutane or ammonia as the reagent gas. Youshould be familiar with operating the CI-equipped 5975 Series MSD with

methane reagent gas before attempting to use other reagent gases.

Do not use nitrous oxide as a reagent gas It radically shortens the life span of the




Changing the reagent gas from methane to either isobutane or ammonia

changes the chemistry of the ionization process and yields different ions. The

principal chemical ionization reactions encountered are described in general

in Appendix A, “Chemical Ionization Theory . If you are not experienced with

chemical ionization, we suggest reviewing that material before you proceed.

CAUTIONDo not use nitrous oxide as a reagent gas. It radically shortens the life span of the

filament.

CAUTION Not all setup operations can be performed in all modes with all reagent gases. SeeTable 18 for details.


Table 18 Reagent gases

Reagent gas/mode Reagent ion masses PFDTDCalibrant ions

Flow adj ions: RatioEI/PCI/NCI MSD

Performance turbo

pump

Recommended flow:

20% PCI




Isobutane CIIsobutane (C4H10) is commonly used for chemical ionization when less

fragmentation is desired in the chemical ionization spectrum. This is because

the proton affinity of isobutane is higher than that of methane; hence less

energy is transferred in the ionization reaction.

Addition and proton transfer are the ionization mechanisms most often

associated with isobutane. The sample itself influences which mechanism

dominates.

40% NCI

Methane/PCI 17, 29, 41*

* There are no PFDTD ions formed with any reagent gas but methane. Tune with methane and usethe same parameters for the other gas.

41, 267, 599 28/27: 1.5 – 5.0

Methane/NCI 17, 35, 235†

† There are no negative reagent gas ions formed. To pretune in negative mode, use backgroundions: 17 (OH-), 35 (Cl-), and 235 (ReO3-). These ions can not be used for reagent gas flow adjust-ment. Set flow to 40% for NCI and adjust as necessary to get acceptable results for your appli-cation.

185, 351, 449 N/A

Isobutane/PCI 39, 43, 57 N/A 57/43: 5.0 – 30.0

Isobutane/NCI 17, 35, 235 185, 351, 449 N/A

Ammonia/PCI 18, 35, 52 N/A 35/18: 0.1 – 1.0

Ammonia/NCI 17, 35, 235 185, 351, 517 N/A


Ammonia CI

Ammonia (NH3) is commonly used for chemical ionization when less

fragmentation is desired in the chemical ionization spectrum. This is becausethe proton affinity of ammonia is higher than that of methane; hence less

energy is transferred in the ionization reaction.

Because many compounds of interest have insufficient proton affinities,

ammonia chemical-ionization spectra often result from the addition of NH4+




a o a c e ca o at o spect a o te esu t o t e add t o o N 4

and then, in some cases, from the subsequent loss of water. Ammonia reagent

ion spectra have principal ions at m/z 18, 35, and 52, corresponding to NH4+,

NH4(NH3)+, and NH4(NH3)2+.

To adjust your MSD for isobutane or ammonia chemical ionization, use the

following procedure:

Procedure

1 From the Tune and Vacuum Control view, perform a standard Positive CI

autotune with methane and PFDTD.

2 Under the Setup menu, click CI Tune Wizard and when prompted select

Isobutane or Ammonia. This will change the menus to use the selected gas and

select appropriate default tune parameters.

3 Select Gas B. Follow the instructions and prompts from the Tune Wizard

and set the gas flow to 20%.

If you use an existing tune file, be sure to save it with a new name if you

don’t want to overwrite the existing values. Accept the default temperatureand other settings.

4 Click Isobutane (or Ammonia) Flow Adjust on the Setup menu.

There is no CI autotune for isobutane or ammonia in PCI.

If you wish to run NCI with isobutane or ammonia, load NCICH4.U or an

existing NCI tune file for the specific gas.

NOTEBe sure to read the following application note: Implementation of Ammonia Reagent

Gas for Chemical Ionization on the Agilent 5975 Series MSDs (5989-5170EN).


CAUTIONUse of ammonia affects the maintenance requirements of the MSD. See “CI

Maintenance” for more information.

CAUTIONThe pressure of the ammonia supply must be less than 5 psig. Higher pressures can

result in ammonia condensing from a gas to a liquid.




Ammonia tends to break down vacuum pump fluids and seals. Ammonia CI

makes more frequent vacuum system maintenance necessary. (See the 5975

Series MSD Troubleshooting and Maintenance Manual.)

Frequently, a mixture of 5% ammonia and 95% helium or 5% ammonia and 95%

methane is used as a CI reagent gas. This is enough ammonia to achieve good

chemical ionization while minimizing its negative effects.

Carbon dioxide CI

Carbon dioxide is often used as a reagent gas for CI. It has obvious advantages

of availability and safety.

Always keep the ammonia tank in an upright position, below the level of the flow

module. Coil the ammonia supply tubing into several vertical loops by wrapping the

tubing around a can or bottle. This will help keep any liquid ammonia out of the flowmodule.

CAUTIONWhen running ammonia for 5 or more hours a day, the foreline pump must be ballasted

(flushed with air) for at least 1 hour a day to minimize damage to pump seals. Always

purge the MSD with methane after flowing ammonia.


To switch from the CI source to the EI source

Procedure

1 From the Tune and Vacuum Control view, vent the MSD. See page 82. The

software will prompt you for the appropriate actions.

2 Open the analyzer.

3 Remo e the CI interface tip seal See page 143




3 Remove the CI interface tip seal. See page 143.

4 Remove the CI ion source. See page 142.

5 Install the EI ion source. See page 136.

6 Place the CI ion source and interface tip seal in the ion source storage box.


8 Load your EI tune file.

CAUTIONAlways wear clean gloves while touching the analyzer or any other parts that go inside

the analyzer chamber.



and take other antistatic precautions before you open the analyzer chamber.

See page 131.


CI Autotune

After the reagent gas flow is adjusted, the lenses and electronics of the MSDshould be tuned (Table 19). Perfluoro-5,8-dimethyl-3,6,9-trioxidodecane

(PFDTD) is used as the calibrant. Instead of flooding the entire vacuum

chamber, the PFDTD is introduced directly into the ionization chamber

through the GC/MSD interface by means of the gas flow control module.




There is a PCI autotune for methane only, as there are no PFDTD ions

produced by other gases in positive mode. PFDTD ions are visible in NCI for

any reagent gas. Always tune for methane PCI first regardless of which mode

or reagent gas you wish to use for your analysis.

There are no tune performance criteria. If CI autotune completes, it passes.

EMVolts (electron multiplier voltage) at or above 2600 V, however, indicates a

problem. If your method requires EMVolts set at +400, you may not have

adequate sensitivity in your data acquisition.

CAUTIONAfter the source is changed from EI to CI or vented for any other reason, the MSD must

be purged and baked out for at least 2 hours before tuning. Longer bakeout isrecommended before running samples requiring optimal sensitivity.

CAUTIONAlways verify MSD performance in EI before switching to CI operation. See page 76.



Table 19 Reagent gas settings

Reagent gas Methane Isobutane Ammonia EI

Ion polarity Positive Negative Positive Negative Positive Negative N/A

Emission 150 A 50 A 150 A 50 A 150 A 50 A 35 A

Electron

energy

150 eV 150 eV 150 eV 150 eV 150 eV 150 eV 70 eV




energy

Filament 1 1 1 1 1 1 1 or 2

Repeller 3 V 3 V 3 V 3 V 3 V 3 V 30 V

Ion focus 130 V 130 V 130 V 130 V 130 V 130 V 90 V

Entrance

lens offset

20 V 20 V 20 V 20 V 20 V 20 V 25 V

EM volts 1200 1400 1200 1400 1200 1400 1300

Shutoff valve Open Open Open Open Open Open Closed

Gas select A A B B B B None

Suggested

flow

20% 40% 20% 40% 20% 40% N/A

Source temp 250 °C 150 °C 250 °C 150 °C 250 °C 150 °C 230 °C

Quad temp 150 °C 150 °C 150 °C 150 °C 150 °C 150 °C 150 °C

Interfacetemp

280 °C 280 °C 280 °C 280 °C 280 °C 280 °C 280 °C

Autotune Yes Yes No Yes No Yes Yes

N/A Not available


To perform a PCI autotune (methane only)

Procedure






Procedure

1 Verify that the MSD performs correctly in EI mode first. See page 76.

2 Load the PCICH4.U tune file (or an existing tune file for the reagent gas you

are using).


don’t want to overwrite the existing values.

3 Accept the default settings.

4 Perform methane setup. See page 109.

5 Under the Tune menu, click CI Autotune.

There are no tune performance criteria. If autotune completes, it passes(Figure 30). If the tune sets the electron multiplier voltage (EMVolts) at or

above 2600 V, however, you may not be able to acquire data successfully if your

method sets EMVolts to “+400” or higher.

The autotune report contains information about air and water in the system.

The 19/29 ratio shows the abundance of water.

The 32/29 ratio shows the abundance of oxygen.

CAUTIONAvoid tuning more often than is absolutely necessary; this will minimize PFDTD

background noise and help prevent ion source contamination.





Figure 30 PCI autotune


To perform an NCI autotune (methane reagent gas)

P d


Always set up the CI MSD in PCI with methane as the reagent gas first, even if you are

going to be using a different reagent gas or going to run NCI.




Procedure

1 From the Tune and Vacuum Control view, load NCICH4.U (or an existing tunefile for the reagent gas you are using).

2 From the Setup menu select the CI Tune Wizard and follow the system

prompts.

Accept the default temperature and other settings.


don’t want to overwrite the existing values.

3 Under the Tune menu, click CI Autotune.

There are no tune performance criteria. If autotune completes, it passes(Figure 31). If the tune sets the electron multiplier voltage (EMVolts) at or

above 2600 V, however, you may not be able to acquire data successfully if your

method sets EMVolts to “+400” or higher.

CAUTIONAvoid tuning unless absolutely necessary; this will minimize PFDTD background noise

and help prevent ion source contamination.





Figure 31 NCI autotune


To verify PCI performance

Materials needed

• Benzophenone, 100 pg/L (8500-5440)






Procedure

1 Verify that the MSD performs correctly in E1 mode.

2 Verify that the PCICH4.U tune file is loaded.

3 Select Gas A and set flow to 20%.

4 In Tune and Vacuum Control view, perform CI setup. See page 116.

5 Run CI Autotune. See page 116.

6 Run the PCI sensitivity method BENZ_PCI.M using 1 µL of 100 pg/µL

benzophenone.

7 Verify that the system conforms to the published sensitivity specification.



To verify NCI performance

This procedure is for EI/PCI/NCI MSDs only.

Materials needed

• Octafluoronaphthalene (OFN), 100 fg/µL (5188-5347)

Always verify MSD performance in EI before switching to CI operation See page 76

http://www.agilent.com/chem






Procedure

1 Verify that the MSD performs correctly in EI mode.

2 Load the NCICH4.U tune file, and accept the temperature setpoints.

3 Select Gas A and set flow to 40%.

4 In Tune and Vacuum Control view, run CI Autotune. See page 120.

Note that there are no criteria for a “passing” Autotune in CI. If the

Autotune completes, it passes.

5 Run the NCI sensitivity method: OFN_NCI.M using 2 µL of 100 fg/µL OFN.

6 Verify that the system conforms to the published sensitivity specification.





To monitor high vacuum pressure

Procedure

WARNINGIf you are using hydrogen as a carrier gas, do not turn on the Micro-Ion vacuum

gauge if there is any possibility that hydrogen has accumulated in the manifold.

Read “Hydrogen Safety” before operating the MSD with hydrogen carrier gas.







Procedure

1 Start up and pump down the MSD. See page 103.2 In the Tune and Vacuum Control view select Turn Vacuum Gauge on/off from

the Vacuum menu.

3 In the Instrument Control view you can set up an MS Monitor for reading.

The vacuum can also be read on the LCP or from the Manual Tune screen.

The gauge controller will not turn on if the pressure in the MSD is above

approximately 8 × 10-3 Torr. The gauge controller is calibrated for nitrogen, but

all pressures listed in this manual are for helium.

The largest influence on operating pressure is the carrier gas (column) flow.

Table 20 lists typical pressures for various helium carrier gas flows. These

pressures are approximate and will vary from instrument to instrument.


Typical pressure readings

Use the G3397A Micro-Ion vacuum gauge. Note that the mass flow controller is

calibrated for methane and the vacuum gauge is calibrated for nitrogen, sothese measurements are not accurate, but are intended as a guide to typical

observed readings (Table 20). They were taken with the following set of

conditions. Note that these are typical PCI temperatures:

Source temperature 250 °CQuad temperature 150 °CI f 280 °C




Familiarize yourself with the measurements on your system under operating

conditions and watch for changes that may indicate a vacuum or gas f low

problem. Measurements will vary by as much as 30% from one MSD and gauge

controller to the next.

Interface temperature 280 °CHelium carrier gas flow 1 mL/min

Table 20 Flow and pressure readings

Pressure (Torr)

Methane Ammonia

MFC(%)

EI/PCI/NCI MSD(Performance turbo pump)

EI/PCI/NCI MSD(Performance turbo pump)

10 5.5 ×10 –5 5.0 ×10 –5

15 8.0 ×10 –5 7.0 ×10 –5

20 1.0 ×10 –4 8.5 ×10 –5

25 1.2 ×10 –4 1.0 ×10 –4

30 1.5 ×1 –4 1.2 ×10 –4

35 2.0 ×10 –4 1.5 ×10 –4

40 2.5 ×10 –4 2.0 ×10 –4






Operation Manual

5

General Maintenance

Before Starting 128

Maintaining the Vacuum System 133





Before Starting

You can perform much of the maintenance required by your MSD. For yoursafety, read all of the information in this introduction before performing any

maintenance tasks.

Scheduled maintenance

Common maintenance tasks are listed in Table 21. Performing these tasks

when scheduled can reduce operating problems, prolong system life, and

d ll ti t




reduce overall operating costs.

Keep a record of system performance (tune reports) and maintenance

operations performed. This makes it easier to identify variations from normal

operation and to take corrective action.

Table 21 Maintenance schedule

Task Every week Every 6 months Every year As needed

Tune the MSD X

Check the foreline pump oil level X

Check the calibration vial(s) X

Replace the foreline pump oil* X

Replace the diffusion pump fluid X

Check the dry foreline pump X

Clean the ion source X

Check the carrier gas trap(s) on the GC and

MSD

X

Replace the worn out parts X

Lubricate sideplate or vent valve O-rings† X

Replace CI Reagent gas supply X

Replace GC gas supplies X

* Every 3 months for CI MSDs using ammonia reagent gas.

† Vacuum seals other than the side plate O-ring and vent valve O-ring do not need to be lubricated. Lubricating other sealscan interfere with their correct function.

General Maintenance 5

Tools, spare parts, and supplies

Some of the required tools, spare parts, and supplies are included in the GC

shipping kit, MSD shipping kit, or MSD tool kit. You must supply others yourself. Each maintenance procedure includes a list of the materials required

for that procedure.

High voltage precautions

Whenever the MSD is plugged in, even if the power switch is off, potentially

dangerous voltage (120 VAC or 200/240 VAC) exists on:




dangerous voltage (120 VAC or 200/240 VAC) exists on:

• The wiring and fuses between where the power cord enters the instrument

and the power switch

When the power switch is on, potentially dangerous voltages exist on:

• Electronic circuit boards

• Toroidal transformer

• Wires and cables between these boards

• Wires and cables between these boards and the connectors on the back

panel of the MSD

• Some connectors on the back panel (for example, the foreline power

receptacle)

Normally, all of these parts are shielded by safety covers. As long as the safety

covers are in place, it should be difficult to accidentally make contact with

dangerous voltages.

Some procedures in this chapter require access to the inside of the MSD while

the power switch is on. Do not remove any of the electronics safety covers inany of these procedures. To reduce the risk of electric shock, follow the

procedures carefully.

WARNINGPerform no maintenance with the MSD turned on or plugged into its power source

unless you are instructed to by one of the procedures in this chapter.


Dangerous temperatures

Many parts in the MSD operate at, or reach, temperatures high enough to

cause serious burns. These parts include, but are not limited to:• GC/MSD interface

• Analyzer parts

• Vacuum pumps

WARNINGNever touch these parts while your MSD is on. After the MSD is turned off, give




The GC inlets and GC oven also operate at very high temperatures. Use the

same caution around these parts. See the documentation supplied with your

GC for more information.

Chemical residue

Only a small portion of your sample is ionized by the ion source. The majority

of any sample passes through the ion source without being ionized. It is

pumped away by the vacuum system. As a result, the exhaust from the forelinepump will contain traces of the carrier gas and your samples. Exhaust from

the standard foreline pump also contains tiny droplets of foreline pump oil.

An oil trap is supplied with the standard foreline pump. This trap stops only

pump oil droplets. It does not trap any other chemicals. If you are using toxic

solvents or analyzing toxic chemicals, do not use this oil trap. For all foreline

WARNING

these parts enough time to cool before handling them.

WARNINGThe GC/MSD interface heater is powered by a thermal zone on the GC. The interface

heater can be on, and at a dangerously high temperature, even though the MSD is

off. The GC/MSD interface is well insulated. Even after it is turned off, it cools very

slowly.

WARNINGThe foreline pump can cause burns if touched when operating. It has a safety shield

to prevent the user from touching it.


pumps, install a hose to take the exhaust from the foreline pump outdoors or

into a fume hood vented to the outdoors. For the standard foreline pump, this

requires removing the oil trap. Be sure to comply with your local air quality

regulations.

WARNINGThe oil trap supplied with the standard foreline pump stops only foreline pump oil. It

does not trap or filter out toxic chemicals. If you are using toxic solvents or

analyzing toxic chemicals, remove the oil trap. Do not use the trap if you have a CI

MSD. Install a hose to take the foreline pump exhaust outside or to a fume hood.




The fluids in the diffusion pump and standard foreline pump also collect

traces of the samples being analyzed. All used pump fluid should be

considered hazardous and handled accordingly. Dispose of used fluid

correctly, as specified by your local regulations.

Electrostatic discharge

All of the printed circuit boards in the MSD contain components that can be

damaged by electrostatic discharge (ESD). Do not handle or touch these

boards unless absolutely necessary. In addition, wires, contacts, and cables

can conduct ESD to the electronics boards to which they are connected. This is

especially true of the mass filter (quadrupole) contact wires which can carry

ESD to sensitive components on the side board. ESD damage may not cause

immediate failure but it will gradually degrade the performance and stability

of your MSD.

When you work on or near printed circuit boards or when you work on

components with wires, contacts, or cables connected to printed circuit

boards, always use a grounded antistatic wrist strap and take other antistaticprecautions. The wrist strap should be connected to a known good earth

ground. If that is not possible, it should be connected to a conductive (metal)

part of the assembly being worked on, but not to electronic components,

exposed wires or traces, or pins on connectors.

WARNINGWhen replacing pump fluid, use appropriate chemical-resistant gloves and safety

glasses. Avoid all contact with the fluid.


Take extra precautions, such as a grounded antistatic mat, if you must work

on components or assemblies that have been removed from the MSD. This

includes the analyzer.

CAUTIONTo be effective, an antistatic wrist strap must fit snugly (not tight). A loose strap

provides little or no protection.

Antistatic precautions are not 100% effective. Handle electronic circuit boards as little

as possible and then only by the edges. Never touch components, exposed traces, or

pins on connectors and cables.





Maintaining the Vacuum System

Periodic maintenance As listed earlier in Table 21, some maintenance tasks for the vacuum system

must be performed periodically. These include:

• Checking the foreline pump fluid (every week)

• Checking the calibration vial(s) (every 6 months)

• Ballasting the foreline pump (daily in MSDs using ammonia reagent gas)




• Replacing the foreline pump oil (every 6 months; every 3 months for CIMSDs using ammonia reagent gas)

• Tightening the foreline pump oil box screws (first oil change after

installation)

• Replacing the diffusion pump fluid (once a year)

• Replacing the dry foreline pump (typically every 3 years)

Failure to perform these tasks as scheduled can result in decreasedinstrument performance. It can also result in damage to your instrument.

Other procedures

Tasks such as replacing a foreline vacuum gauge or Micro-Ion vacuum gauge

should be performed only when needed. See the 5975 Series MSD

Troubleshooting and Maintenance manual and see the online help in the MSD

ChemStation software for symptoms that indicate this type of maintenance isrequired.

More information is available

If you need more information about the locations or functions of vacuum

system components, see the 5975 Series MSD Troubleshooting and

Maintenance manual.

Most of the procedures in this chapter are illustrated with video clips on the

Agilent GC/GCMSD Hardware User Information & Instrument Utilities and

5975 Series MSD User Information disks.


To remove the EI ion source

Materials needed


• Large (8650-0030)

• Small (8650-0029)

• Pliers, long-nose (8710-1094)

Procedure




1 Vent the MSD. See page 82.

2 Open the analyzer chamber. See page 84.

Make sure you use an antistatic wrist strap and take other antistatic

precautions before touching analyzer components.

3 Disconnect the seven wires from the ion source. Do not bend the wires any

more than necessary (Figure 32 and Table 22).

Table 22 Ion source wires

Wire color Connects to Number of leads

Blue Entrance lens 1

Orange Ion focus 1

White Filament 1 (top

filament)

2

Red Repeller 1

Black Filament 2 (bottom

filament)

2

CAUTIONPull on the connectors, not on the wires.


4 Trace the wires for the ion source heater and temperature sensor to the

feedthrough board. Disconnect them there.

5 Remove the thumbscrews that hold the ion source in place.

6 Pull the ion source out of the source radiator.

WARNINGThe analyzer operates at high temperatures. Do not touch any part until you are sure

it is cool.

http://localhost/var/www/apps/conversion/tmp/Videos/Remove%20the%20EI%20ion%20source.wmv






Figure 32 Removing the ion source

Source feedthrough board

Ion source

Thumbscrews

Source heater and temperature sensor wires

Source radiator


To reinstall the EI ion source

Materials needed


• Large (8650-0030)

• Small (8650-0029)

• Pliers, long-nose (8710-1094)

Procedure

http://localhost/var/www/apps/conversion/tmp/Videos/Install%20Analyzer%20source.wmv




1 Slide the ion source into the source radiator (Figure 33).

2 Install and hand tighten the source thumbscrews. Do not overtighten the

thumbscrews.

3 Connect the ion source wires as shown in “To close the analyzer chamber” .

Close the analyzer chamber.









Figure 33 Installing the EI ion source

Ion source

Thumbscrews

Source radiator






Operation Manual

6

CI Maintenance

General Information 140

Ion source cleaning 140

Ammonia 140

To Set Up Your MSD for CI Operation 141

G id li 141




Guidelines 141To install the CI ion source 142

To install the CI interface tip seal 143

This chapter describes maintenance procedures and requirements that are

unique to 5975 Series MSDs equipped with the Chemical Ionization hardware.

6 CI Maintenance

General Information

Ion source cleaningThe main effect of operating the MSD in CI mode is the need for more frequent

ion source cleaning. In CI operation, the ion source chamber is subject to more

rapid contamination than in EI operation because of the higher source

pressures required for CI.

WARNING

Always perform any maintenance procedures using hazardous solvents under a

fume hood Be sure to operate the MSD in a well ventilated room




Ammonia

Ammonia, used as a reagent gas, increases the need for foreline pump

maintenance. Ammonia causes foreline pump oil to break down more quickly.

Therefore, the oil in the standard foreline vacuum pump must be checked andreplaced more frequently.

Always purge the MSD with methane after using ammonia.

Be sure to install the ammonia so the tank is in an upright position. This will

help prevent liquid ammonia from getting into the flow module.

WARNING fume hood. Be sure to operate the MSD in a well-ventilated room.

CI Maintenance 6

To Set Up Your MSD for CI Operation

Setting up your MSD for operation in CI mode requires special care to avoid

contamination and air leaks.

Guidelines

• Before venting in EI mode, verify that the GC/MSD system is performing

correctly. See “To verify system performance” .

• Make sure the reagent gas inlet line(s) are equipped with gas purifiers (not

applicable for ammonia)




applicable for ammonia).

• Use extra-high purity reagent gases; 99.99% or better for methane and as

pure as is available for other reagent gases.

6 CI Maintenance

To install the CI ion source

Procedure

1 Vent the MSD and open the analyzer. See page 84.

2 Remove the EI ion source See page 134

CAUTION Electrostatic discharges to analyzer components are conducted to the side boardwhere they can damage sensitive components. Wear a grounded antistatic wrist strap


http://localhost/var/www/apps/conversion/tmp/Videos/InstallCIsource.wmv






2 Remove the EI ion source. See page 134.3 Remove the CI ion source from its storage box and insert the ion source into

the radiator.

4 Reinstall the thumbscrews (Figure 34).

5 Connect the wiring as described in “To close the analyzer chamber” .

Figure 34 Installing the CI ion source

Ion source

Thumbscrews

Source radiator

CI Maintenance 6

To install the CI interface tip seal

Materials needed

• Interface tip seal (G1099-60412)

The interface tip seal must be in place for CI operation. It is necessary to

achieve adequate ion source pressure for CI.










Procedure

1 Remove the seal from the ion source storage box.

2 Verify that the CI ion source is installed.

3 Place the seal over the end of the interface. To remove the seal, reverse theabove steps.

4 Gently check the alignment of the analyzer and the interface.

When the analyzer is aligned correctly, the analyzer can be closed all the

way with no resistance except the spring tension from the interface tip seal.

5 You can align the analyzer and interface by wiggling the side plate on its

hinge. If the analyzer still will not close, contact your Agilent Technologies

service representative.

a d ta e ot e a t stat c p ecaut o s you ope t e a a y e c a be

CAUTION

Forcing the analyzer closed if these parts are misaligned will damage the seal or the

interface or the ion source, or will keep the sideplate from sealing.

6 CI Maintenance

http://localhost/var/www/apps/conversion/tmp/Videos/CIInterfaceTip.wmv







Operation Manual

A

Chemical Ionization Theory

Chemical Ionization Overview 146

Positive CI Theory 148

Negative CI Theory 155





Chemical Ionization Overview

Chemical ionization (CI) is a technique for creating ions used in mass

spectrometric analyses. There are significant differences between CI and

electron ionization (EI). This section describes the most common chemical

ionization mechanisms.

In EI, relatively high-energy electrons (70 eV) collide with molecules of the

sample to be analyzed. These collisions produce (primarily) positive ions.

Upon ionization, the molecules of a given substance fragment in fairly

predictable patterns. EI is a direct process; energy is transferred by collision

from electrons to the sample molecules.




For CI, in addition to the sample and carrier gas, large amounts of reagent gas

are introduced into the ionization chamber. Since there is so much more

reagent gas than sample, most of the emitted electrons collide with reagent gas

molecules, forming reagent ions. These reagent-gas ions react with each other

in primary and secondary reaction processes that establish an equilibrium.

They also react in various ways with sample molecules to form sample ions. CI

ion formation involves much lower energy and is much more “gentle” thanelectron ionization. Since CI results in much less fragmentation, CI spectra

usually show high abundance of the molecular ion. For this reason, CI is often

used to determine the molecular weights of sample compounds.

Methane is the most common CI reagent gas. It yields certain characteristic

ionization patterns. Other reagent gases yield different patterns and may

result in better sensitivity for some samples. Common alternative reagent

gases are isobutane and ammonia. Carbon dioxide is often used in negative CI.

Less common reagent gases are carbon dioxide, hydrogen, Freon,

trimethylsilane, nitric oxide, and methylamine. Different ionization reactions

occur with each reagent gas.

Water contamination in reagent gases will decrease CI sensitivity

dramatically. A large peak at m/z 19 (H30+) in positive CI is a diagnostic

symptom of water contamination. In high enough concentrations, especially

when combined with calibrant, water contamination will result in a heavily

WARNINGAmmonia is toxic and corrosive. Use of ammonia requires special maintenance and

safety precautions.

Chemical Ionization Theory A

contaminated ion source. Water contamination is most common immediately

after new reagent gas tubing or reagent gas cylinders are connected. This

contamination will often decrease if the reagent gas is allowed to flow for a

few hours, purging the system.

References on chemical ionization

A. G. Harrison, Chemical Ionization Mass Spectrometry, 2nd Edition, CRC

Press, INC. Boca Raton, FL (1992) ISBN 0-8493-4254-6.

W. B. Knighton, L. J. Sears, E. P. Grimsrud, “High Pressure Electron Capture

Mass Spectrometry”, Mass Spectrometry Reviews (1996), 14, 327-343.

E A Stemmler R A Hites Electron Capture Negative Ion Mass Spectra of




E. A. Stemmler, R. A. Hites, Electron Capture Negative Ion Mass Spectra of

Environmental Contaminants and Related Compounds, VCH Publishers,

New York, NY (1988) ISBN 0-89573-708-6.


Positive CI Theory

Positive CI (PCI) occurs with the same analyzer voltage polarities as EI. For

PCI, the reagent gas is ionized by collision with emitted electrons. The reagent

gas ions react chemically with sample molecules (as proton donors) to form

sample ions. PCI ion formation is more “gentle” than electron ionization,

producing less fragmentation. This reaction usually yields high abundance of

the molecular ion and is therefore often used for determining molecular

weights of samples.

The most common reagent gas is methane. Methane PCI produces ions with

almost any sample molecule. Other reagent gases, such as isobutane orammonia are more selective and cause even less fragmentation Because of




ammonia, are more selective and cause even less fragmentation. Because of

the high background from the reagent gas ions, PCI is not especially sensitive

and detection limits are generally high.

There are four fundamental ionization processes that take place during

positive chemical ionization at ion source pressures in the 0.8 to 2.0 Torr

range. These are:

• Proton transfer

• Hydride abstraction

• Addition

• Charge exchange

Depending on the reagent gas used, one or more of these four processes can be

used to explain the ionization products observed in the resulting mass spectra.

EI, methane PCI, and ammonia PCI spectra of methyl stearate are shown in

Figure 35. The simple fragmentation pattern, large abundance of the [MH]+

ion, and the presence of the two adduct ions are characteristic of positive

chemical ionization using methane as a reagent gas.

The presence of air or water in the system, especially in the presence of

PFDTD calibrant, quickly contaminates the ion source.





Figure 35 Methyl stearate (MW = 298): EI, methane PCI, and ammonia PCI


Proton transfer

Proton transfer can be expressed as

BH+ + M MH+ + B

where the reagent gas B has undergone ionization resulting in protonation. If

the proton affinity of the analyte (sample) M is greater than that of the reagent

gas, then the protonated reagent gas will transfer its proton to the analyte

forming a positively charged analyte ion.

The most frequently used example is the proton transfer from CH5+ to the

molecular analyte, which results in the protonated molecular ion MH+.

The relative proton affinities of the reagent gas and the analyte govern the




proton transfer reaction. If the analyte has a greater proton affinity than the

reagent gas, then proton transfer can take place. Methane (CH4) is the most

common reagent gas because its proton affinity is very low.

Proton affinities can be defined according to the reaction:

B + H+ BH+

where the proton affinities are expressed in kcal/mole. Methane's proton

affinity is 127 kcal/mole. Tables 23 and 24 list the proton affinities of several

possible reagent gases and of several small organic compounds with various

functional groups.

The mass spectrum generated by a proton-transfer reaction depends on

several criteria. If the difference in proton affinities is large (as with methane),

substantial excess energy may be present in the protonated molecular ion.

This can result in subsequent fragmentation. For this reason, isobutane with a

proton affinity of 195 kcal/mole may be preferred to methane for some

analyses. Ammonia has a proton affinity of 207 kcal/mole, making it less likely

to protonate most analytes. Proton-transfer chemical ionization is usually

considered to be “soft” ionization, but the degree of the softness depends on

the proton affinities of both the analyte and the reagent gas, as well as on

other factors including ion source temperature.


Table 23 Reagent gas proton affinities

Species Proton affinity

kcal/mole

Reactant ion

formed

H2 100 H3+ (m/z 3)

CH4 127 CH5+ (m/z 17)

C2H4 160 C2H5+ (m/z 29)

H2O 165 H3O+ (m/z 19)

H2S 170 H3S+ (m/z 35)

CH3OH 182 CH3OH2+ (m/z 33)




CH3OH 182 CH3OH2 (m/z 33)

t-C4H10 195 t-C4H9+ (m/z 57)

NH3 207 NH4+ (m/z 18)

Table 24 Proton affinities of selected organic compounds for PCI

Molecule Proton affinity

(kcal/mole)


(kcal/mole)

Acetaldehyde 185 Methyl amine 211

Acetic acid 188 Methyl chloride 165

Acetone 202 Methyl cyanide 186Benzene 178 Methyl sulfide 185

2-Butanol 197 Methyl cyclopropane l80

Cyclopropane 179 Nitroethane 185

Dimethyl ether 190 Nitromethane 180

Ethane 121 n-Propyl acetate 207

Ethyl formate 198 Propylene 179

Formic acid 175 Toluene 187

Hydrobromic acid 140 trans-2-Butene 180

Hydrochloric acid 141 Trifluoroacetic acid 167


Isopropyl alcohol 190 Xylene 187

Methanol 182

Table 24 Proton affinities of selected organic compounds for PCI (continued)


(kcal/mole)


(kcal/mole)





Hydride abstraction

In the formation of reagent ions, various reactant ions can be formed that have

high hydride-ion (H–) affinities. If the hydride-ion affinity of a reactant ion is

higher than the hydride-ion affinity of the ion formed by the analyte's loss of

H–, then the thermodynamics are favorable for this chemical ionization

process. Examples include the hydride abstraction of alkanes in methane

chemical ionization. In methane CI, both CH5+ and C2H5

+ are capable of

hydride abstraction. These species have large hydride-ion affinities, which

results in the loss of H– for long-chain alkanes, according to the general

reaction

R+ + M [M–H]+ + RH

For methane R+ is CH5+ and C2H5

+ and M is a long-chain alkane In the case




For methane, R is CH5 and C2H5 , and M is a long chain alkane. In the case

of CH5+, the reaction proceeds to form [M–H]+ + CH 4+ H2. The spectra

resulting from hydride abstraction will show an M–1 m/z peak resulting from

the loss of H–. This reaction is exothermic so fragmentation of the [M–H]+ ion

is often observed.

Often, both hydride-abstraction and proton-transfer ionization can be evident

in the sample spectrum. One example is the methane CI spectrum of

long-chain methyl esters, where both hydride abstraction from the

hydrocarbon chain and proton transfer to the ester function occur. In the

methane PCI spectrum of methyl stearate, for example, the MH+ peak at

m/z 299 is created by proton transfer and the [M–1]+ peak at m/z 297 is

created by hydride abstraction.

AdditionFor many analytes, proton-transfer and hydride-abstraction chemical

ionization reactions are not thermodynamically favorable. In these cases,

reagent gas ions are often reactive enough to combine with the analyte

molecules by condensation or association (addition reactions). The resulting

ions are called adduct ions. Adduct ions are observed in methane chemical

ionization by the presence of [M+C2H5]+ and [M+C3H5]+ ions, which result in

M+29 and M+41 m/z mass peaks. Addition reactions are particularly important in ammonia CI. Because the

NH3 has a high proton affinity, few organic compounds will undergo proton

transfer with ammonia reagent gas. In ammonia CI, a series of ion-molecule

reactions takes place, resulting in the formation of NH4+, [NH4NH3]+, and

[NH4(NH3)2]+. In particular, the ammonium ion, NH4+, will give rise to an


intense [M+NH4]+ ion observed at M+18 m/z , either through condensation or

association. If this resulting ion is unstable, subsequent fragmentation may be

observed. The neutral loss of H2O or NH3, observed as a subsequent loss of 18

or 17 m/z , respectively, is also common.

Charge exchange

Charge-exchange ionization can be described by the reaction:

X+· + M M+· + X

where X+ is the ionized reagent gas and M is the analyte of interest. Examples

of reagent gases used for charge exchange ionization include the noble gases(helium, neon, argon, krypton, xenon, and radon), nitrogen, carbon dioxide,

carbon monoxide hydrogen and other gases that do not react “chemically”




carbon monoxide, hydrogen, and other gases that do not react chemically

with the analyte. Each of these reagent gases, once ionized, has a

recombination energy expressed as:

X+· + e– X

or simply the recombination of the ionized reagent with an electron to form a

neutral species. If this energy is greater than the energy required to remove anelectron from the analyte, then the first reaction above is exothermic and

thermodynamically allowed.

Charge-exchange chemical ionization is not widely used for general analytical

applications. It can, however, be used in some cases when other chemical

ionization processes are not thermodynamically favored.


Negative CI Theory

Negative chemical ionization (NCI) is performed with analyzer voltage

polarities reversed to select negative ions. There are several chemicalmechanisms for NCI. Not all mechanisms provide the dramatic increases in

sensitivity often associated with NCI. The four most common mechanisms

(reactions) are:

• Electron capture

• Dissociative electron capture

• Ion pair formation

• Ion-molecule reactions

I ll f th t th i l l ti th t




In all of the cases except the ion-molecule reactions, the reagent gas serves a

function different from the function it serves in PCI. In NCI, the reagent gas is

often referred to as the buffer gas. When the reagent gas is bombarded with

high energy electrons from the filament, the following reaction occurs:

Reagent gas + e– (230eV) Reagent ions + e– (thermal)

If the reagent gas is methane (Figure 36), the reaction is:

CH4 + e– (230eV) CH4+ + 2e–

(thermal)

The thermal electrons have lower energy levels than the electrons from the

filament. It is these thermal electrons that react with the sample molecules.

There are no negative reagent gas ions formed. This prevents the kind of

background that is seen in PCI mode and is the reason for the much lower

detection limits of NCI. The products of NCI can only be detected when the

MSD is operating in negative ion mode. This operating mode reverses the

polarity of all the analyzer voltages.

Carbon dioxide is often used as a buffer gas in NCI. It has obvious cost,

availability, and safety advantages over other gases.





Figure 36 Endosulfan I (MW = 404): EI and methane NCI


Electron capture

Electron capture is the primary mechanism of interest in NCI. Electron

capture (often referred to as high-pressure electron capture mass

spectrometry or HPECMS) provides the high sensitivity for which NCI isknown. For some samples under ideal conditions, electron capture can provide

sensitivity as much as 10 to 1000 times higher than positive ionization.

Note that all the reactions associated with positive CI will also occur in NCI

mode, usually with contaminants. The positive ions formed do not leave the

ion source because of the reversed lens voltages, and their presence can

quench the electron capture reaction.

The electron capture reaction is described by:

MX + e–(th l) MX–·




MX + e (thermal) MX

where MX is the sample molecule and the electron is a thermal (slow) electron

generated by the interaction between high energy electrons and the reagent

gas.

In some cases, the MX–

·radical anion is not stable. In those cases the reverse

reaction can occur:

MX–· MX + e–

The reverse reaction is sometimes called autodetachment. This reverse

reaction generally occurs very quickly. Thus, there is little time for the

unstable anion to be stabilized through collisions or other reactions.

Electron capture is most favorable for molecules that have hetero-atoms. For

example: nitrogen, oxygen, phosphorus, sulfur, silicon, and especially thehalogens: fluorine, chlorine, bromine, and iodine.

The presence of oxygen, water, or almost any other contaminant interferes

with the electron-attachment reaction. Contaminants cause the negative ion to

be formed by the slower ion-molecule reaction. This generally results in less

sensitivity. All potential contamination sources, especially oxygen (air) and

water sources, must be minimized.


Dissociative electron capture

Dissociative electron capture is also known as dissociative resonance capture.

It is a process similar to electron capture. The difference is that during the

reaction, the sample molecule fragments or dissociates. The result is typically an anion and a neutral radical. Dissociative electron capture is illustrated by

the reaction equation:

MX + e–(thermal) M· + X–

This reaction does not yield the same sensitivity as electron capture, and the

mass spectra generated typically have lower abundance of the molecular ion.

As with electron capture, the products of dissociative electron capture are not always stable. The reverse reaction sometimes occurs. This reverse reaction is

sometimes called an associative detachment reaction. The equation for the




sometimes called an associative detachment reaction. The equation for the

reverse reaction is:

M· + X– MX + e–

Ion pair formation

Ion pair formation is superficially similar to dissociative electron capture. The

ion pair formation reaction is represented by the equation:

MX + e–(thermal) M+ + X¯ + e–

As with dissociative electron capture, the sample molecule fragments. Unlike

dissociative electron capture however, the electron is not captured by the

fragments. Instead, the sample molecule fragments in such a way that the

electrons are distributed unevenly and positive and negative ions aregenerated.


Ion-molecule reactions

Ion-molecule reactions occur when oxygen, water, and other contaminants are

present in the CI ion source. Ion-molecule reactions are two to four times

slower than electron-attachment reactions and do not provide the highsensitivity associated with electron capture reactions. Ion-molecule reactions

can be described by the general equation:

M + X– MX–

where X– is most often a halogen or hydroxyl group that was created by

ionization of contaminants by electrons from the filament. Ion-molecule

reactions compete with electron capture reactions. The more ion-molecule

reactions that occur, the fewer electron capture reactions occur.

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